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Title :   STRUCTURE OF GLUTAMATE DEHYDROGENASE

Authors :   K. S. P. Yip, T. J. Stillman, K. L. Britton, A. Pasquo, D. W. Rice

Date :   22 Aug 96 (Deposition) - 11 Jan 97 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)

Keywords :   Oxidoreductase, Nad, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Yip, T. J. Stillman, K. L. Britton, P. J. Artymiuk, P. J. Baker, S. E. Sedelnikova, P. C. Engel, A. Pasquo, R. Chiaraluce, V. Consalvi, R. Scandurra, D. W. Rice
The Structure Of Pyrococcus Furiosus Glutamate Dehydrogenas Reveals A Key Role For Ion-Pair Networks In Maintaining Enzyme Stability At Extreme Temperatures.
Structure V. 3 1147 1995
PubMed-ID: 8591026 | Reference-DOI: 10.1016/S0969-2126(01)00251-9
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE DEHYDROGENASE
	Chains	:	A, B, C
	EC Number	:	1.4.1.3
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:244 , SER A:245 , LYS A:264	BINDING SITE FOR RESIDUE SO4 A 420
2	AC2	SOFTWARE	GLY B:221 , ASN B:222 , ALA B:223	BINDING SITE FOR RESIDUE SO4 B 420
3	AC3	SOFTWARE	GLY C:221 , ASN C:222 , ALA C:223	BINDING SITE FOR RESIDUE SO4 C 420
4	AC4	SOFTWARE	ASP B:244 , SER B:245 , LYS B:246 , LYS B:264	BINDING SITE FOR RESIDUE SO4 B 421
5	AC5	SOFTWARE	GLY A:221 , ASN A:222 , ALA A:223 , HOH A:482	BINDING SITE FOR RESIDUE SO4 A 421
6	AC6	SOFTWARE	ASP C:244 , SER C:245 , LYS C:246 , LYS C:264 , HOH C:437	BINDING SITE FOR RESIDUE SO4 C 421

(no "SS Bond" information available for 1GTM)

(no "Cis Peptide Bond" information available for 1GTM)

(no "SAP(SNP)/Variant" information available for 1GTM)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLFV_DEHYDROGENASE	PS00074	Glu / Leu / Phe / Val dehydrogenases active site.	DHE3_PYRFU	99-112	3	A:98-111 B:98-111 C:98-111

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLFV_DEHYDROGENASE	PS00074	Glu / Leu / Phe / Val dehydrogenases active site.	DHE3_PYRFU	99-112	6	A:98-111 B:98-111 C:98-111

(no "Exon" information available for 1GTM)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:417
 aligned with DHE3_PYRFU | P80319 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       
           DHE3_PYRFU     4 QDPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 420
               SCOP domains d1gtma2 A:3-180 Glutamate dehydrogenase                                                                                                                                           d1gtma1 A:181-419 Glutamate dehydrogenase                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------1gtmA01 A:35-180 Leucine Dehydrogenase, chain A, domain 1                                                                                         1gtmA02 A:181-418 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhh...eeeeeeeeee.....eeeeeeeeeeee....eee..eee.....hhhhhhhhhhhhhhhhh....eeeeeeeee..hhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh.....hhhh.....hhh........hhhhhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhh....eeeeee....eee......hhhhhhhhhhh.........eee.hhhhhh....eeee..........hhhh....eee........hhhhhhhhh...eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------GLFV_DEHYDROGE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gtm A   3 ADPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain B from PDB  Type:PROTEIN  Length:417
 aligned with DHE3_PYRFU | P80319 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       
           DHE3_PYRFU     4 QDPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 420
               SCOP domains d1gtmb2 B:3-180 Glutamate dehydrogenase                                                                                                                                           d1gtmb1 B:181-419 Glutamate dehydrogenase                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------1gtmB01 B:35-180 Leucine Dehydrogenase, chain A, domain 1                                                                                         1gtmB02 B:181-418 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhh....eeeeeeeeee.....eeeeeeeeeeee....eee..eeee....hhhhhhhhhhhhhhhhh....eeeeeeeee..hhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh.....hhhh.....hhh........hhhhhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhh..eeeeee....eee......hhhhhhhhhhh.........eee.hhhhhh....eeee........hhhhhh....eee........hhhhhhhhh...eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------GLFV_DEHYDROGE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gtm B   3 ADPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain C from PDB  Type:PROTEIN  Length:417
 aligned with DHE3_PYRFU | P80319 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       
           DHE3_PYRFU     4 QDPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 420
               SCOP domains d1gtmc2 C:3-180 Glutamate dehydrogenase                                                                                                                                           d1gtmc1 C:181-419 Glutamate dehydrogenase                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------1gtmC01 C:35-180 Leucine Dehydrogenase, chain A, domain 1                                                                                         1gtmC02 C:181-418 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhh...eeeeeeeeee.....eeeeeeeeeeee....eee..eee.....hhhhhhhhhhhhhhhhh....eeeeeeee...hhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh.....hhhh.....hhh........hhhhhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhh..eeeeeee..eeee......hhhhhhhhhhh.........eee.hhhhhh....eeee........hhhhhh....eee........hhhhhhhhh...eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------GLFV_DEHYDROGE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gtm C   3 ADPYEIVIKQLERAAQYMEISEEALEFLKRPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTWKTAVMDLPYGGGKGGIIVDPKKLSDREKERLARGYIRAIYDVISPYEDIPAPDVYTNPQIMAWMMDEYETISRRKTPAFGIITGKPLSIGGSLGRIEATARGASYTIREAAKVLGWDTLKGKTIAIQGYGNAGYYLAKIMSEDFGMKVVAVSDSKGGIYNPDGLNADEVLKWKNEHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITKKNADNIKAKIVAEVANGPVTPEADEILFEKGILQIPDFLCNAGGVTVSYFEWVQNITGYYWTIEEVRERLDKKMTKAFYDVYNIAKEKNIHMRDAAYVVAVQRVYQAMLDRGWVKH 419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "Pfam Domain" information available for 1GTM)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DHE3_PYRFU | P80319)

molecular function
	GO:0004353	glutamate dehydrogenase [NAD(P)+] activity	Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016639	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Biological Unit
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