Structure of PDB 5ess Chain D

Receptor sequence
>5essD (length=542) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence]
NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHV
RIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLI
VLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNA
TWRSATCRVLAAATGARTANAGPVHFDIPLREPTPPGRPAGKPWTYTPPV
TFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPL
ALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQ
ATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAV
SHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAI
GAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSL
TIVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVES
RQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL
3D structure
PDB5ess Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
ChainD
Resolution2.2 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) C26 E55
Catalytic site (residue number reindexed from 1) C25 E54
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 TOG D S377 N378 R381 R399 A402 G403 I404 D405 G439 D440 L441 T442 D469 G471 G472 G473 I474 F475 S365 N366 R369 R387 A390 G391 I392 D393 G427 D428 L429 T430 D457 G459 G460 G461 I462 F463
BS02 MG D D440 D469 G471 D428 D457 G459
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

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Biological Process
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Cellular Component
External links
PDB RCSB:5ess, PDBe:5ess, PDBj:5ess
PDBsum5ess
PubMed27291649
UniProtP9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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