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(-) Description

Title :  GLUTAMATE DEHYDROGENASE
 
Authors :  K. L. Britton, P. J. Baker, T. J. Stillman, D. W. Rice
Date :  03 Apr 96  (Deposition) - 12 Mar 97  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Oxidoreductase, Nad (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)

(-) Compounds

Molecule 1 - GLUTAMATE DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.4.1.2
    Organism Scientific: CLOSTRIDIUM SYMBIOSUM
    Organism Taxid: 1512
    Strain: HB25

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1HRD)

(-) Sites  (0, 0)

(no "Site" information available for 1HRD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLFV_DEHYDROGENASEPS00074 Glu / Leu / Phe / Val dehydrogenases active site.DHE2_CLOSY120-133
 
 		  3A:119-132
B:119-132
C:119-132
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLFV_DEHYDROGENASEPS00074 Glu / Leu / Phe / Val dehydrogenases active site.DHE2_CLOSY120-133
 
 		  6A:119-132
B:119-132
C:119-132

(-) Exons   (0, 0)

(no "Exon" information available for 1HRD)

(-) Sequences/Alignments

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:449
 aligned with DHE2_CLOSY | P24295 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:449
                                    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 450
               SCOP domains d1hrda2 A:1-194 Glutamate dehydrogenase                                                                                                                                                           d1hrda1 A:195-449 Glutamate dehydrogenase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1hrdA03 A:1-51,A:425-449                           1hrdA02 A:52-187 Leucine Dehydrogenase, chain A, domain 1                                                                               -------------------1hrdA01 A:207-373 NAD(P)-binding Rossmann-like Domain                                                                                                                  ---------------------------------------------------1hrdA03 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........hhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhh...eeeeeee..eeee.......hhhhhhhhhhhhh....hhhhhhhh..eeee..........eee.........hhhhhhhhh....eee........hhhhhhhhh....eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------GLFV_DEHYDROGE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hrd A   1 SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW 449
                                    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         


Chain B from PDB  Type:PROTEIN  Length:449
 aligned with DHE2_CLOSY | P24295 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:449
                                    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 450
               SCOP domains d1hrdb2 B:1-194 Glutamate dehydrogenase                                                                                                                                                           d1hrdb1 B:195-449 Glutamate dehydrogenase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1hrdB03 B:1-51,B:425-449                           1hrdB02 B:52-187 Leucine Dehydrogenase, chain A, domain 1                                                                               -------------------1hrdB01 B:207-373 NAD(P)-binding Rossmann-like Domain                                                                                                                  ---------------------------------------------------1hrdB03 B:1-51,B:425-449  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhh..hhhhh....eeeeeeeeee.....eeeeeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh....hhh.....hhh........hhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh...eeeeeee..eeee.......hhhhhhhhhhhhh....hhhhhhhh..eeee...hhh....eeee........hhhhhhhhh....eee........hhhhhhhhh....eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------GLFV_DEHYDROGE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hrd B   1 SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW 449
                                    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         


Chain C from PDB  Type:PROTEIN  Length:449
 aligned with DHE2_CLOSY | P24295 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:449
                                    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 450
               SCOP domains d1hrdc2 C:1-194 Glutamate dehydrogenase                                                                                                                                                           d1hrdc1 C:195-449 Glutamate dehydrogenase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1hrdC03 C:1-51,C:425-449                           1hrdC02 C:52-187 Leucine Dehydrogenase, chain A, domain 1                                                                               -------------------1hrdC01 C:207-373 NAD(P)-binding Rossmann-like Domain                                                                                                                  ---------------------------------------------------1hrdC03 C:1-51,C: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.....hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhh..eeeeeee..eeee.......hhhhhhhhhhhhh....hhhhhhhh..eeee...hhh....eee.........hhhhhhhhh....eee........hhhhhhhhh....eee.hhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------GLFV_DEHYDROGE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hrd C   1 SKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLVRPEATGYGSVYYVEAVMKHENDTLVGKTVALAGFGNVAWGAAKKLAELGAKAVTLSGPDGYIYDPEGITTEEKINYMLEMRASGRNKVQDYADKFGVQFFPGEKPWGQKVDIIMPCATQNDVDLEQAKKIVANNVKYYIEVANMPTTNEALRFLMQQPNMVVAPSKAVNAGGVLVSGFEMSQNSERLSWTAEEVDSKLHQVMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW 449
                                    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
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 9)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DHE2_CLOSY | P24295: 1aup 1bgv 1k89 2yfh

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