Structure of PDB 5z2r Chain B

Receptor sequence
>5z2rB (length=556) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
MSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHH
THFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKL
ILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVS
TIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWL
REAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIG
DVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQAS
CEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIP
RLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVKLIDAL
SQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLN
ALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHA
AAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLL
AQVSHL
3D structure
PDB5z2r Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
ChainB
Resolution2.3 Å
3D
structure
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Enzymatic activity
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 TD6 B E55 Q118 E55 Q118
BS02 TD6 B N390 S391 L392 R413 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474 F475 N390 S391 L392 R413 I418 D419 G441 D442 L443 S444 Y447 N469 G471 G472 Q473 I474 F475
BS03 MG B D442 N469 G471 D442 N469 G471
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0030976 thiamine pyrophosphate binding
GO:0042803 protein homodimerization activity
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5z2r, PDBe:5z2r, PDBj:5z2r
PDBsum5z2r
PubMed30341164
UniProtP17109|MEND_ECOLI 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)

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