1BGV - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   GLUTAMATE DEHYDROGENASE

Authors :   T. J. Stillman, P. J. Baker, K. L. Britton, D. W. Rice

Date :   01 Jun 98 (Deposition) - 14 Oct 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

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

Reference :   T. J. Stillman, P. J. Baker, K. L. Britton, D. W. Rice
Conformational Flexibility In Glutamate Dehydrogenase. Role Of Water In Substrate Recognition And Catalysis.
J. Mol. Biol. V. 234 1131 1993
PubMed-ID: 8263917 | Reference-DOI: 10.1006/JMBI.1993.1665
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.4.1.2
	Organism Scientific	:	CLOSTRIDIUM SYMBIOSUM
	Organism Taxid	:	1512
	Other Details	:	THE RESIDUE LABELLED B 501, A GLUTAMATE, IS THE ENZYME'S SUBSTRATE WHICH IS BOUND WITHIN THE ACTIVE SITE. IT IS THOUGHT TO AN ONLY PARTIALLY OCCUPIED SITE AND SO ITS OCCUPANCY WAS SET TO 0.53.

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GLU	1	Mod. Amino Acid	GLUTAMIC ACID

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	GLU	6	Mod. Amino Acid	GLUTAMIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:89 , GLY A:91 , GLN A:110 , LYS A:113 , LYS A:125 , ALA A:163 , GLY A:164 , ASP A:165 , SER A:380 , HOH A:502	BINDING SITE FOR RESIDUE GLU A 501

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLFV_DEHYDROGENASE	PS00074	Glu / Leu / Phe / Val dehydrogenases active site.	DHE2_CLOSY	120-133	1	A:119-132

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.	DHE2_CLOSY	120-133	6	A:119-132

(no "Exon" information available for 1BGV)

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:450
 aligned with DHE2_CLOSY | P24295 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          450 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441        |-
           DHE2_CLOSY     2 SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW-   -
               SCOP domains d1bgva2 A:1-194 Glutamate dehydrogenase                                                                                                                                                           d1bgva1 A:195-449 Glutamate dehydrogenase                                                                                                                                                                                                                      - SCOP domains
               CATH domains 1bgvA03 A:1-51,A:425-449                           1bgvA02 A:52-187 Leucine Dehydrogenase, chain A, domain 1                                                                               -------------------1bgvA01 A:207-373 NAD(P)-binding Rossmann-like Domain                                                                                                                  ---------------------------------------------------1bgvA03 A:1-51,A:425-449 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhh....eeeeeeeeee.....eeeeeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh....hhh.....hhh.....hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhh..eeeeeee..eeee.......hhhhhhhhhhhhh....hhhhhhhh..eeee...hhh....eeee........hhhhhhhhh....eeee.......hhhhhhhhh....eee.hhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------GLFV_DEHYDROGE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bgv A   1 SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAWE 501
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          449|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           501

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 1BGV)

Asymmetric Unit(hide GO term definitions)

Chain A (DHE2_CLOSY | P24295)

molecular function
	GO:0004352	glutamate dehydrogenase (NAD+) activity	Catalysis of the reaction: L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH + 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:0019552	glutamate catabolic process via 2-hydroxyglutarate	The anaerobic chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate 2-hydroxyglutarate, yielding energy in the form of ATP.
	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.

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	DHE2_CLOSY \| P24295	:	1aup 1hrd 1k89 2yfh

(no "Related Entries Specified in the PDB File" available for 1BGV)

Description

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Ligands, Modified Residues, Ions (1, 1)

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