Structure of PDB 2vdc Chain D

Receptor sequence

>2vdcD (length=1472) Species: 192 (Azospirillum brasilense)

CGVGFIAAIDGKPRRSVVEKGIEALKAVWHRGAVDADGKTGDGAGIHVAV
PQKFFKDHVKVIGHRAPDNKLAVGQVFLPRISLDAQEACRCIVETEILAF
GYYIYGWRQVPINVDIIGEKANATRPEIEQIIVGNNKGVSDEQFELDLYI
IRRRIEKAVKGEQINDFYICSLSARSIIYKGMFLAEQLTTFYPDLLDERF
ESDFAIYHQRYSTNTFPTWPLAQPFRMLAHNGEINTVKGNVNWMKAHETR
MEHPAFGTHMQDLKPVIGVGLSDSGSLDTVFEVMVRAGRTAPMVKMMLVP
QALTSSQTTPDNHKALIQYCNSVMEPWDGPAALAMTDGRWVVGGMDRNGL
RPMRYTITTDGLIIGGSETGMVKIDETQVIEKGRLGPGEMIAVDLQSGKL
YRDRELKDHLATLKPWDKWVQNTTHLDELVKTASLKGEPSDMDKAELRRR
QQAFGLTMEDMELILHPMVEDGKEAIGSMGDDSPIAVLSDKYRGLHHFFR
QNFSQVTNPPIDSLRERRVMSLKTRLGNLGNILDEDETQTRLLQLESPVL
TTAEFRAMRDYMGDTAAEIDATFPVDGGPEALRDALRRIRQETEDAVRGG
ATHVILTDEAMGPARAAIPAILATGAVHTHLIRSNLRTFTSLNVRTAEGL
DTHYFAVLIGVGATTVNAYLAQEAIAERHRRGLFGSMPLEKGMANYKKAI
DDGLLKIMSKMGISVISSYRGGGNFEAIGLSRALVAEHFPAMVSRISGIG
LNGIQKKVLEQHATAYNEEVVALPVGGFYRFRKSGDRHGWEGGVIHTLQQ
AVTNDSYTTFKKYSEQVNKRPPMQLRDLLELRSTKAPVPVDEVESITAIR
KRFITPGMSMGALSPEAHGTLNVAMNRIGAKSDSGEGGEDPARFRPDKNG
DNWNSAIKQVASGRFGVTAEYLNQCRELEIKVAQGAKPGEGGQLPGFKVT
EMIARLRHSTPGVMLISPPPHHDIYSIEDLAQLIYDLKQINPDAKVTVKL
VSRSGIGTIAAGVAKANADIILISGNSGGTGASPQTSIKFAGLPWEMGLS
EVHQVLTLNRLRHRVRLRTDGGLKTGRDIVIAAMLGAEEFGIGTASLIAM
GCIMVRQCHSNTCPVGVCVQDDKLRQKFVGTPEKVVNLFTFLAEEVREIL
AGLGFRSLNEVIGRTDLLHQVSRGAEHLDDLDLNPRLAQVDPGENARYCT
LQGRNEVPDTLDARIVADARPLFEEGEKMQLAYNARNTQRAIGTRLSSMV
TRKFGMFGLQPGHITIRLRGTAGQSLGAFAVQGIKLEVMGDANDYVGKGL
SGGTIVVRPTTSSPLETNKNTIIGNTVLYGATAGKLFAAGQAGERFAVRN
SGATVVVEGCGSNGCEYMTGGTAVILGRVGDNFAAGMTGGMAYVYDLDDS
LPLYINDESVIFQRIEVGHYESQLKHLIEEHVTETQSRFAAEILNDWARE
VTKFWQVVPKEMLNRLEVPVHL

3D structure

• PDB: 2vdc The Subnanometer Resolution Structure of the Glutamate Synthase 1.2-Mda Hexamer by Cryoelectron Microscopy and its Oligomerization Behavior in Solution: Functional Implications.
• Chain: D
• Resolution: 9.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C1 R31 Y211 N231 G232 M479 E886 Q934 K937 Q943
• Catalytic site (residue number reindexed from 1): C1 R31 Y211 N231 G232 M479 E886 Q934 K937 Q943
• Enzyme Commision number: 1.4.1.13: glutamate synthase (NADPH).

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	OMT	D	R210 N231 G232 E233 D273	R210 N231 G232 E233 D273
BS02	FMN	D	P856 G857 M858 S859 E886 Q909 K931 K999 G1028 G1029 T1030 G1031 D1070 G1071 G1072 G1093 T1094	P856 G857 M858 S859 E886 Q909 K931 K999 G1028 G1029 T1030 G1031 D1070 G1071 G1072 G1093 T1094
BS03	AKG	D	S859 K937 G942 R957 T1030 G1031	S859 K937 G942 R957 T1030 G1031
BS04	F3S	D	C1102 Q1107 C1108 C1113 V1117 C1118	C1102 Q1107 C1108 C1113 V1117 C1118

Gene Ontology

Molecular Function

• GO:0004355 glutamate synthase (NADPH) activity
• GO:0015930 glutamate synthase activity
• GO:0016491 oxidoreductase activity
• GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors
• GO:0046872 metal ion binding
• GO:0051538 3 iron, 4 sulfur cluster binding

Biological Process

• GO:0006537 glutamate biosynthetic process
• GO:0006541 glutamine metabolic process
• GO:0019676 ammonia assimilation cycle
• GO:0097054 L-glutamate biosynthetic process

External links

• PDB: RCSB:2vdc, PDBe:2vdc, PDBj:2vdc
• PDBsum: 2vdc
• PubMed: 18199747
• UniProt: Q05755|GLTB_AZOBR Glutamate synthase [NADPH] large chain (Gene Name=gltB)