DB code: D00489

CATH domain 3.20.20.30 : TIM Barrel Catalytic domain
3.20.20.30 : TIM Barrel
E.C. 1.14.14.3
CSA 1luc
M-CSA 1luc
MACiE M0132

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P07739 Alkanal monooxygenase beta chain
EC 1.14.14.3
Bacterial luciferase beta chain
PF00296 (Bac_luciferase)
[Graphical View]
P07740 Alkanal monooxygenase alpha chain
EC 1.14.14.3
Bacterial luciferase alpha chain
PF00296 (Bac_luciferase)
[Graphical View]

KEGG enzyme name
alkanal monooxygenase (FMN-linked)
bacterial luciferase
aldehyde monooxygenase
luciferase
Vibrio fischeri luciferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07740 LUXA_VIBHA RCHO + reduced FMN + O(2) = RCOOH + FMN + H(2)O + light. Heterodimer of an alpha and a beta chain.
P07739 LUXB_VIBHA RCHO + reduced FMN + O(2) = RCOOH + FMN + H(2)O + light. Heterodimer of an alpha and a beta chain.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00071 C01847 C00007 C00060 C00061 C00001 C00205
E.C.
Compound Magnesium Aldehyde Reduced FMN O2 Carboxylate FMN H2O hn(light)
Type divalent metal (Ca2+, Mg2+) carbohydrate amide group,amine group,aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ion others carboxyl group amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ion H2O others
ChEBI 18420
16048
15379
26689
27140
17621
15377
PubChem 888
101960650
445395
711
977
643976
22247451
962
1brlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1lucA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound Unbound
1brlB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bslA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bslB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1lucB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound Unbound
1xkjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1xkjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [17], [20], [21], [26] & [33]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1brlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 44;HIS 45;CYS 106;ASP 113;PHE 261 GLU 19(Magnesium binding) ALA 74;ALA 75
1lucA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 44;HIS 45;CYS 106;ASP 113;PHE 261 GLU 19(Magnesium binding) ALA 74;ALA 75
1brlB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)
1bslA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)
1bslB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)
1lucB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)
1xkjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)
1xkjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 237(Magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
SCHEME I
[7]
SCHEME I, SCHEME II
[9]
Scheme 1
[11]
p.1771-1773
[12]
Scheme 1, p.12199-12200
[13]
p.1920
[14]
p.6584-6586
[16]
Fig.1
[17]
p.1967
[18]
SCHEME I, SCHEME II, SCHEME III, SCHEME IV, SCHEME VI, p.108-110
[20]
Scheme 1, p.14612-14614
[21]
p.671-672
[23]
Fig.1, Fig.9, p.2604-2605
[26]
Scheme I, p.4413-4415
[31]
p.1566-1569
[33]
Scheme 1, p.1728-2730

References
[1]
Resource
Comments
Medline ID
PubMed ID 5161031
Journal Biochemistry
Year 1971
Volume 10
Pages 4069-73
Authors Meighen EA, Nicoli MZ, Hastings JW
Title Functional differences of the nonidentical subunits of bacterial luciferase. Properties of hybrids of native and chemically modified bacterial luciferase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 5056080
Journal Biochemistry
Year 1972
Volume 11
Pages 3359-70
Authors Cline TW, Hastings JW
Title Mutationally altered bacterial luciferase. Implications for subunit functions.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 4822498
Journal J Biol Chem
Year 1974
Volume 249
Pages 2385-92
Authors Nicoli MZ, Meighen EA, Hastings JW
Title Bacterial luciferase. Chemistry of the reactive sulfhydryl.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6965792
Journal Proc Natl Acad Sci U S A
Year 1980
Volume 77
Pages 249-52
Authors Tu SC, Hastings JW
Title Physical interaction and activity coupling between two enzymes induced by immobilization of one.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3968061
Journal J Biol Chem
Year 1985
Volume 260
Pages 1287-9
Authors Swanson R, Weaver LH, Remington SJ, Matthews BW, Baldwin TO
Title Crystals of luciferase from Vibrio harveyi. A preliminary characterization.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2307667
Journal J Biol Chem
Year 1990
Volume 265
Pages 4200-3
Authors Xi L, Cho KW, Herndon ME, Tu SC
Title Elicitation of an oxidase activity in bacterial luciferase by site-directed mutation of a noncatalytic residue.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 1567836
Journal Biochemistry
Year 1992
Volume 31
Pages 3807-13
Authors Abu-Soud H, Mullins LS, Baldwin TO, Raushel FM
Title Stopped-flow kinetic analysis of the bacterial luciferase reaction.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 1560468
Journal J Mol Biol
Year 1992
Volume 224
Pages 523-6
Authors Moore SA, James MN, O'Kane DJ, Lee J
Title Crystallization of Photobacterium leiognathi non-fluorescent flavoprotein, an unusual flavoprotein with limited sequence identity to bacterial luciferase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8422349
Journal Biochemistry
Year 1993
Volume 32
Pages 404-11
Authors Eckstein JW, Hastings JW, Ghisla S
Title Mechanism of bacterial bioluminescence: 4a,5-dihydroflavin analogs as models for luciferase hydroperoxide intermediates and the effect of substituents at the 8-position of flavin on luciferase kinetics.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8494880
Journal Biochemistry
Year 1993
Volume 32
Pages 5036-44
Authors Sinclair JF, Waddle JJ, Waddill EF, Baldwin TO
Title Purified native subunits of bacterial luciferase are active in the bioluminescence reaction but fail to assemble into the alpha beta structure.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 8491169
Journal EMBO J
Year 1993
Volume 12
Pages 1767-74
Authors Moore SA, James MN, O'Kane DJ, Lee J
Title Crystal structure of a flavoprotein related to the subunits of bacterial luciferase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 7918440
Journal Biochemistry
Year 1994
Volume 33
Pages 12194-201
Authors Xin X, Xi L, Tu SC
Title Probing the Vibrio harveyi luciferase beta subunit functionality and the intersubunit domain by site-directed mutagenesis.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 7703838
Journal Protein Sci
Year 1994
Volume 3
Pages 1914-26
Authors Moore SA, James MN
Title Common structural features of the luxF protein and the subunits of bacterial luciferase: evidence for a (beta alpha)8 fold in luciferase.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID 95275854
PubMed ID 7756289
Journal Biochemistry
Year 1995
Volume 34
Pages 6581-6
Authors Fisher AJ, Raushel FM, Baldwin TO, Rayment I
Title Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution.
Related PDB 1brl
Related UniProtKB P07739 P07740
[15]
Resource
Comments
Medline ID
PubMed ID 7578121
Journal Biochemistry
Year 1995
Volume 34
Pages 15084-90
Authors Li Z, Meighen EA
Title Tryptophan 250 on the alpha subunit plays an important role in flavin and aldehyde binding to bacterial luciferase. Effects of W-->Y mutations on catalytic function.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8749369
Journal Curr Opin Struct Biol
Year 1995
Volume 5
Pages 798-809
Authors Baldwin TO, Christopher JA, Raushel FM, Sinclair JF, Ziegler MM, Fisher AJ, Rayment I
Title Structure of bacterial luciferase.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS)
Medline ID 96355591
PubMed ID 8703001
Journal J Biol Chem
Year 1996
Volume 271
Pages 21956-68
Authors Fisher AJ, Thompson TB, Thoden JB, Baldwin TO, Rayment I
Title The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.
Related PDB 1luc
Related UniProtKB P07739 P07740
[18]
Resource
Comments
Medline ID
PubMed ID 8550543
Journal J Biol Chem
Year 1996
Volume 271
Pages 104-10
Authors Francisco WA, Abu-Soud HM, Topgi R, Baldwin TO, Raushel FM
Title Interaction of bacterial luciferase with 8-substituted flavin mononucleotide derivatives.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 9048575
Journal Biochemistry
Year 1997
Volume 36
Pages 1891-9
Authors Clark AC, Raso SW, Sinclair JF, Ziegler MM, Chaffotte AF, Baldwin TO
Title Kinetic mechanism of luciferase subunit folding and assembly.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 9402752
Journal Biochemistry
Year 1997
Volume 36
Pages 14609-15
Authors Huang S, Tu SC
Title Identification and characterization of a catalytic base in bacterial luciferase by chemical rescue of a dark mutant.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID 97172895
PubMed ID 9020763
Journal Biochemistry
Year 1997
Volume 36
Pages 665-72
Authors Tanner JJ, Miller MD, Wilson KS, Tu SC, Krause KL
Title Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding.
Related PDB 1xkj
Related UniProtKB P07739
[22]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS)
Medline ID 97160473
PubMed ID 9007973
Journal Protein Sci
Year 1997
Volume 6
Pages 13-23
Authors Thoden JB, Holden HM, Fisher AJ, Sinclair JF, Wesenberg G, Baldwin TO, Rayment I
Title Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.
Related PDB 1bsl
Related UniProtKB P07739 P07740
[23]
Resource
Comments
Medline ID
PubMed ID 9485410
Journal Biochemistry
Year 1998
Volume 37
Pages 2596-606
Authors Francisco WA, Abu-Soud HM, DelMonte AJ, Singleton DA, Baldwin TO, Raushel FM
Title Deuterium kinetic isotope effects and the mechanism of the bacterial luciferase reaction.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 9622513
Journal Biochemistry
Year 1998
Volume 37
Pages 8614
Authors Huang S, Tu SC
Title Identification and characterization of a catalytic base in bacterial luciferase by chemical rescue of a dark mutant
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 10328774
Journal Anal Biochem
Year 1999
Volume 270
Pages 133-9
Authors Min DJ, Andrade JD, Stewart RJ
Title Specific immobilization of in vivo biotinylated bacterial luciferase and FMN:NAD(P)H oxidoreductase.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 10194361
Journal Biochemistry
Year 1999
Volume 38
Pages 4409-15
Authors Li H, Ortego BC, Maillard KI, Willson RC, Tu SC
Title Effects of mutations of the alpha His45 residue of Vibrio harveyi luciferase on the yield and reactivity of the flavin peroxide intermediate.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 10587436
Journal Biochemistry
Year 1999
Volume 38
Pages 16136-45
Authors Noland BW, Dangott LJ, Baldwin TO
Title Folding, stability, and physical properties of the alpha subunit of bacterial luciferase.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 10721898
Journal J Nutr
Year 2000
Volume 130
Pages 331S-332S
Authors Tu SC, Lei B, Liu M, Tang CK, Jeffers C
Title Probing the mechanisms of the biological intermolecular transfer of reduced flavin.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11735398
Journal Biochemistry
Year 2001
Volume 40
Pages 15153-63
Authors Apuy JL, Park ZY, Swartz PD, Dangott LJ, Russell DH, Baldwin TO
Title Pulsed-alkylation mass spectrometry for the study of protein folding and dynamics: development and application to the study of a folding/unfolding intermediate of bacterial luciferase.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 11735428
Journal Biochemistry
Year 2001
Volume 40
Pages 15436-43
Authors Sparks JM, Baldwin TO
Title Functional implications of the unstructured loop in the (beta/alpha)(8) barrel structure of the bacterial luciferase alpha subunit.
Related PDB
Related UniProtKB
[31]
Resource
Comments
Medline ID
PubMed ID 11468353
Journal Protein Sci
Year 2001
Volume 10
Pages 1563-71
Authors Lin LY, Sulea T, Szittner R, Vassilyev V, Purisima EO, Meighen EA
Title Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data.
Related PDB
Related UniProtKB
[32]
Resource
Comments
Medline ID
PubMed ID 11900533
Journal Biochemistry
Year 2002
Volume 41
Pages 3906-15
Authors Inlow JK, Baldwin TO
Title Mutational analysis of the subunit interface of Vibrio harveyi bacterial luciferase.
Related PDB
Related UniProtKB
[33]
Resource
Comments
Medline ID
PubMed ID 11827516
Journal Biochemistry
Year 2002
Volume 41
Pages 1724-31
Authors Low JC, Tu SC
Title Functional roles of conserved residues in the unstructured loop of Vibrio harveyi bacterial luciferase.
Related PDB
Related UniProtKB
[34]
Resource
Comments
Medline ID
PubMed ID 12445781
Journal J Mol Biol
Year 2002
Volume 324
Pages 457-68
Authors Eichhorn E, Davey CA, Sargent DF, Leisinger T, Richmond TJ
Title Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.
Related PDB
Related UniProtKB
[35]
Resource
Comments
Medline ID
PubMed ID 12627978
Journal Biochemistry
Year 2003
Volume 42
Pages 3105-12
Authors Noland BW, Baldwin TO
Title Demonstration of two independently folding domains in the alpha subunit of bacterial luciferase by preferential ligand binding-induced stabilization.
Related PDB
Related UniProtKB

Comments
This enzyme is composed of two distinct but homologous chains.
Although this enzyme can bind two magnesium ions, they are distant from the active site and not involved in catalysis.
The peptide bond between Ala74-Ala75, which is located at the active-site, has a cis conformation, which is extremely rare for non-proryl peptide bond (see [17]).
E.C. 1.13.12.7 is Another luciferase (firefly luciferase, M00009).

Created Updated
2004-02-19 2009-02-26