DB code: M00347

RLCP classification 3.113.90040.334 : Transfer
CATH domain 3.40.50.980 : Rossmann fold Catalytic domain
3.40.50.980 : Rossmann fold Catalytic domain
2.30.38.10 : Luciferase; domain 3 Catalytic domain
3.30.300.30 : GMP Synthetase; Chain A, domain 3 Catalytic domain
1.10.1200.10 : Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
E.C. 6.1.1.13
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.1200.10 : Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A U00001
2.30.38.10 : Luciferase; domain 3 M00009 M00170
3.30.300.30 : GMP Synthetase; Chain A, domain 3 M00009 M00170
3.40.50.980 : Rossmann fold M00009 M00170

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q81G39 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
NP_831153.1 (Protein)
NC_004722.1 (DNA/RNA sequence)
PF00501 (AMP-binding)
[Graphical View]
P39581 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
NP_391729.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF00501 (AMP-binding)
[Graphical View]
Q99ZA6 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
NP_269435.1 (Protein)
NC_002737.1 (DNA/RNA sequence)
YP_282436.1 (Protein)
NC_007297.1 (DNA/RNA sequence)
PF00501 (AMP-binding)
[Graphical View]
Q5XBN5 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
YP_060361.1 (Protein)
NC_006086.1 (DNA/RNA sequence)
PF00501 (AMP-binding)
[Graphical View]
Q03AZ2 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
YP_806072.1 (Protein)
NC_008526.1 (DNA/RNA sequence)
PF00501 (AMP-binding)
PF13193 (DUF4009)
[Graphical View]
P35854 D-alanine--poly(phosphoribitol) ligase subunit 1
EC 6.1.1.13
D-alanine-activating enzyme
DAE
D-alanine-D-alanyl carrier protein ligase
DCL
PF00501 (AMP-binding)
PF13193 (DUF4009)
[Graphical View]
Q81G41 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
NP_831151.1 (Protein)
NC_004722.1 (DNA/RNA sequence)
PF00550 (PP-binding)
[Graphical View]
P39579 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
NP_391731.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF00550 (PP-binding)
[Graphical View]
P63959 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
NP_269433.1 (Protein)
NC_002737.1 (DNA/RNA sequence)
YP_282434.1 (Protein)
NC_007297.1 (DNA/RNA sequence)
PF00550 (PP-binding)
[Graphical View]
Q5XBN7 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
YP_060359.1 (Protein)
NC_006086.1 (DNA/RNA sequence)
PF00550 (PP-binding)
[Graphical View]
Q03AZ0 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
YP_806074.1 (Protein)
NC_008526.1 (DNA/RNA sequence)
PF00550 (PP-binding)
[Graphical View]
P55153 D-alanine--poly(phosphoribitol) ligase subunit 2
EC 6.1.1.13
D-alanyl carrier protein
DCP
PF00550 (PP-binding)
[Graphical View]
P39580 Protein dltB
None NP_391730.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF03062 (MBOAT)
[Graphical View]
P35855 Protein dltB
Basic membrane protein
BMP
PF03062 (MBOAT)
[Graphical View]
P39578 Protein dltD
None NP_391732.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF04914 (DltD_C)
PF04918 (DltD_M)
PF04915 (DltD_N)
[Graphical View]
P55154 Protein dltD
None PF04918 (DltD_M)
PF04915 (DltD_N)
[Graphical View]

KEGG enzyme name
D-Alanine---poly(phosphoribitol) ligase
D-Alanyl-poly(phosphoribitol) synthetase
D-Alanine: membrane acceptor ligase
D-Alanine-D-alanyl carrier protein ligase
D-Alanine-membrane acceptor ligase
D-Alanine-activating enzyme

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q81G39 DLTA_BACCR ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
P39581 DLTA_BACSU ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
Q99ZA6 DLTA_STRP1 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
Q5XBN5 DLTA_STRP6 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
Q03AZ2 DLTA_LACC3 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
P35854 DLTA_LACRH ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate). Cytoplasm (Probable).
Q81G41 DLTC_BACCR ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
P39579 DLTC_BACSU ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
P63959 DLTC_STRP1 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
Q5XBN7 DLTC_STRP6 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
Q03AZ0 DLTC_LACC3 ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
P55153 DLTC_LACRH ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate).
P39580 DLTB_BACSU
P35855 DLTB_LACRH
P39578 DLTD_BACSU
P55154 DLTD_LACRH

KEGG Pathways
Map code Pathways E.C.
MAP00473 D-Alanine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C01134 C00002 C00133 C00653 C06042 C00020 C00013 C04260 L00075 I00128 I00131
E.C.
Compound Magnesium Phosphopantetheine ATP D-alanine poly(ribitol phosphate) Lipoteichoic acid AMP diphosphate O-D-alanyl-poly(ribitol phosphate) D-alanyl-lipoteichoic acid D-alanine adenylate Peptidyl-Ser-phosphopantetheine-S-D-alanine
Type divalent metal (Ca2+, Mg2+) carbohydrate,peptide/protein,phosphate group/phosphate ion,sulfhydryl group amine group,nucleotide amino acids carbohydrate,phosphate group/phosphate ion,polysaccharide carbohydrate,lipid,phosphate group/phosphate ion,polysaccharide amine group,nucleotide phosphate group/phosphate ion amino acids,carbohydrate,phosphate group/phosphate ion,polysaccharide amino acids,carbohydrate,lipid,phosphate group/phosphate ion,polysaccharide
ChEBI 18420
4222
15422
15570
57416
16027
29888
PubChem 888
115254
5957
71080
7311725
6083
1023
21961011
3dhvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fccA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fceA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3dhvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Bound:DAL-AMP Unbound
3fccA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fceA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_CA Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:AMP Unbound Unbound Unbound Unbound Unbound
3e7xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:AMP Unbound Unbound Unbound Unbound Unbound
3lgxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3dhvA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fccA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fceA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3dhvA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fccA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3fceA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7wA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3e7xA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxC04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3lgxD04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3l8cB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hqbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dv5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [5], [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
3dhvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 160 SER 153 invisible 154-158
3fccA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 160 SER 153 invisible 155-158
3fceA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 160 SER 153 invisible 155-158
3e7wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 159 SER 152
3e7xA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 159 SER 152
3lgxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149 invisible 150-151
3lgxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149 invisible 150-152
3lgxC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149 invisible 150-151
3lgxD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149 invisible 150-151
3l8cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149 invisible 150-152
3l8cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 156 SER 149
3dhvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 298(Magnesium binding) THR 297
3fccA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 298(Magnesium binding) THR 297
3fceA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 298(Magnesium binding) THR 297
3e7wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 297(Magnesium binding) THR 296
3e7xA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 297(Magnesium binding) THR 296
3lgxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3lgxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3lgxC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3lgxD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3l8cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3l8cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 296(Magnesium binding) THR 295
3dhvA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 397
3fccA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 397
3fceA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 397
3e7wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3e7xA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3lgxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3lgxB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3lgxC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3lgxD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3l8cA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3l8cB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 396
3dhvA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 403;ARG 408;LYS 492
3fccA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 403;ARG 408;LYS 492
3fceA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 403;ARG 408;LYS 492
3e7wA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 491
3e7xA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 491
3lgxA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 495
3lgxB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 495
3lgxC04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 495
3lgxD04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 495
3l8cA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;;LYS 495 invisible 403-407
3l8cB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 402;ARG 407;LYS 495
1hqbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 39(Phosphopantetheine covalently binding through phosphate)
1dv5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 39(Phosphopantetheine covalently binding through phosphate)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.4, Fig.5, p.32489-32491
[6]
p.347-349, p.350-353

References
[1]
Resource
Comments
Medline ID
PubMed ID 8300523
Journal J Bacteriol
Year 1994
Volume 176
Pages 681-90
Authors Heaton MP, Neuhaus FC
Title Role of the D-alanyl carrier protein in the biosynthesis of D-alanyl-lipoteichoic acid.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7797557
Journal J Biol Chem
Year 1995
Volume 270
Pages 15598-606
Authors Perego M, Glaser P, Minutello A, Strauch MA, Leopold K, Fischer W
Title Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11434765
Journal Biochemistry
Year 2001
Volume 40
Pages 7964-72
Authors Volkman BF, Zhang Q, Debabov DV, Rivera E, Kresheck GC, Neuhaus FC
Title Biosynthesis of D-alanyl-lipoteichoic acid: the tertiary structure of apo-D-alanyl carrier protein.
Related PDB 1hqb 1dv5
Related UniProtKB Q03AZ0 P55153
[4]
Resource
Comments
Medline ID
PubMed ID 18847223
Journal Biochemistry
Year 2008
Volume 47
Pages 11473-80
Authors Du L, He Y, Luo Y
Title Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus.
Related PDB 3dhv
Related UniProtKB Q81G39
[5]
Resource
Comments
Medline ID
PubMed ID 18784082
Journal J Biol Chem
Year 2008
Volume 283
Pages 32484-91
Authors Yonus H, Neumann P, Zimmermann S, May JJ, Marahiel MA, Stubbs MT
Title Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains.
Related PDB 3e7w 3e7x
Related UniProtKB P39581
[6]
Resource
Comments
Medline ID
PubMed ID 19324056
Journal J Mol Biol
Year 2009
Volume 388
Pages 345-55
Authors Osman KT, Du L, He Y, Luo Y
Title Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP.
Related PDB 3fcc 3fce
Related UniProtKB Q81G39
[7]
Resource
Comments
Medline ID
PubMed ID 19896895
Journal Int J Med Microbiol
Year 2010
Volume 300
Pages 148-54
Authors Xia G, Kohler T, Peschel A
Title The wall teichoic acid and lipoteichoic acid polymers of Staphylococcus aureus.
Related PDB
Related UniProtKB

Comments
This enzyme performs D-alanylation of lipoteichoic acids, which are the components of cell walls for Gram-positive bacteria (see [4], [6] and [7]).
This enzyme is composed of four subunits, DltA (D-alanyl carrier protein ligase, or Dcl), DltC (D-alanyl carrier protein, or Dcp), DltB (an integral membrane protein), and DltD (a membrane-tethered protein via N-terminal transmembrane domain). Although the structures of DltA and DltC have been elucidated, the structures of the two membrane proteins have not been solved yet. The structure of DltC (PDB; 1hqb and 1dv5) must be similar to those with phosphopantetheine from plasmodium (PDB;2fq0 and 2fq2)
According to the literature [5] and [6], this enzyme catalyzes the following reactions:
(A) Transfer of AMP from ATP to D-alanine carboxylate, forming an intermediate, D-ala-AMP, and releasing diphosphate (by DltA):
(A0) The magnesim ion, bound to Glu298 (of 3dhv), stabilizes the negative charge on the leaving beta- and gamma-phosphate groups of ATP. Simultaneously, Arg397 stabilizes the beta-phosphate, whereas the mainchain amide of Ser153 stabilizes the gamma-phosphate group. Meanwhile, the mobile residue, Lys492, stabilizes the transferred alpha-phosphate of ATP, along with the mainchain amide of Thr297, and modulates/stabilizes the acceptor nucleophile, the carboxylate oxygen of D-alanine substrate.
(A1) The carboxylate of D-alanine makes a nucleophilic attack on the alpha-phosphate group of ATP, forming a transition state. The transferred phosphate and leaving diphosphate group can be stabilized by the positively charged residues and magnesium ion during the transition state. (SN2-like reaction).
(B) Transfer of D-alanine group to thiol group of phosphopantetheine, which is covalently bound to a serine sidechain of DltC:
As the complex structure of DltA and DltC has not been elucidated, the detailed mechanism of this reaction is not clear.
(C) Transfer of D-alanine to the hydroxyl group of Lipoteichoic acids:
Although it is not clear how DltB and DltD are involved in the transfer reaction, they seem to be required for hte translocation and incorporation of D-alanine into Lipoteichoic acids.

Created Updated
2012-03-27 2012-05-29