Structure of PDB 1yrq Chain H

Receptor sequence

>1yrqH (length=545) Species: 878 (Solidesulfovibrio fructosivorans)

KPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEI
ILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRN
LVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPG
NSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAH
YLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLAL
SKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPSK
HLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGV
TDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVV
DMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDN
TLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLG
PRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH

3D structure

• PDB: 1yrq Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
• Chain: H
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E25 C72 C75 H79 R476 S499 C543 C546
• Catalytic site (residue number reindexed from 1): E21 C68 C71 H75 R472 S495 C539 C542
• Enzyme Commision number: 1.12.2.1: cytochrome-c3 hydrogenase.

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	F3S	H	K225 Q230	K221 Q226
BS02	SF4	H	R70 H228	R66 H224
BS03	MG	H	E53 L495 H549	E49 L491 H545
BS04	FCO	H	C75 V78 H79 A474 P475 R476 L479 V497 P498 S499 C546	C71 V74 H75 A470 P471 R472 L475 V493 P494 S495 C542

Gene Ontology

Molecular Function

• GO:0008901 ferredoxin hydrogenase activity
• GO:0016151 nickel cation binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0047806 cytochrome-c3 hydrogenase activity

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:1yrq, PDBe:1yrq, PDBj:1yrq
• PDBsum: 1yrq
• PubMed: 15803334
• UniProt: P18188|PHNL_SOLFR Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)