1Q51

Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1q51a_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Cd1q51c_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Jd1q51j_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Ld1q51l_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Bd1q51b_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Dd1q51d_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Ed1q51e_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Fd1q51f_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Gd1q51g_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Hd1q51h_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Id1q51i_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)
Kd1q51k_ Alpha and beta proteins (a/b) ClpP/crotonase ClpP/crotonase Crotonase-like Naphthoate synthase MenB (Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
BSCOP2 FamilyCrotonase-like 8058002 4000036 SCOP2 (2022-06-29)
BSCOP2 SuperfamilyClpP/crotonase 8058003 3000033 SCOP2 (2022-06-29)
DSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyClpP/crotonase 8058003 3000033 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AECH_1e1q51A1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
CECH_1e1q51C1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
JECH_1e1q51J1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
LECH_1e1q51L1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
BECH_1e1q51B1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
DECH_1e1q51D1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
EECH_1e1q51E1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
FECH_1e1q51F1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
GECH_1e1q51G1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
HECH_1e1q51H1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
IECH_1e1q51I1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)
KECH_1e1q51K1 A: a/b three-layered sandwichesX: ClpP/crotonase (From Topology)H: ClpP/crotonase (From Topology)T: ClpP/crotonaseF: ECH_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
A1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
C3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
C1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
J3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
J1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
L3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
L1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
B3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
B1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
D3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
D1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
E3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
E1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
F3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
F1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
G3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
G1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
H3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
H1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
I3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
I1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)
K3.90.226.10 Alpha Beta Alpha-Beta Complex 2-enoyl-CoA Hydratase Chain A, domain 1CATH (4.3.0)
K1.10.12.10 Mainly Alpha Orthogonal Bundle Lyase 2-enoyl-coa Hydratase Chain A, domain 2CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF00378Enoyl-CoA hydratase/isomerase (ECH_1)Enoyl-CoA hydratase/isomeraseThis family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
menB

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR001753Enoyl-CoA hydratase/isomeraseFamily
A, B, C, D, E
IPR029045ClpP/crotonase-like domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR0101981,4-Dihydroxy-2-naphthoyl-CoA synthase, MenBFamily
A, B, C, D, E
IPR014748Enoyl-CoA hydratase, C-terminalHomologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
A, D
1,4-dihydroxy-2-naphthoyl-CoA synthase  M-CSA #346

Naphthoate synthase (MenB, also known as 1,4-dihydroxy-2-naphthoyl-CoA synthase) is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (EC:3.1.2.28). It is a member of the crotonase superfamily.

Defined by 6 residues: GLY:A-105TYR:A-115GLY:A-161ASP:A-185SER:A-190TYR:D-287
Some residues are not modelled and lack atomic coordinates. Visualization is not available.
Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available.
EC: 4.1.3.36 (PDB Primary Data)