Structure of PDB 5eso Chain A

Receptor sequence

>5esoA (length=529) Species: 83332 (Mycobacterium tuberculosis H37Rv)

MNPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLH
VRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPL
IVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALN
ATWRSATCRVLAAATGARTANAGPVHFDIPLREPLVPDPVTPPGRPAGKP
WTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSG
DNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWP
DVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTG
LHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGID
GTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPT
EPIPRSLTIVVSNDNDVSSRIFHDVDVGALCRAYHVESRQIEVDELGPTL
DQPAGMRVLEVKADRSSLRQLHAAIKAAL

3D structure

• PDB: 5eso Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
• Chain: A
• Resolution: 2.05 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C26 E55
• Catalytic site (residue number reindexed from 1): C26 E55
• Enzyme Commision number: 2.2.1.9: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ISC	A	S29 R30 T78 R107 Q118	S29 R30 T78 R107 Q118
BS02	TPP	A	P27 E55	P27 E55

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016740 transferase activity
• GO:0030145 manganese ion binding
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0070204 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity

Biological Process

• GO:0009234 menaquinone biosynthetic process

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:5eso, PDBe:5eso, PDBj:5eso
• PDBsum: 5eso
• PubMed: 27291649
• UniProt: P9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)