1GDH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION

Authors :   J. D. Goldberg, T. Yoshida, P. Brick

Date :   22 Sep 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase(Choh (D)-Nad(P)+ (A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Goldberg, T. Yoshida, P. Brick
Crystal Structure Of A Nad-Dependent D-Glycerate Dehydrogenase At 2. 4 A Resolution.
J. Mol. Biol. V. 236 1123 1994
PubMed-ID: 8120891 | Reference-DOI: 10.1016/0022-2836(94)90016-7
(for further references see the PDB file header)

Molecule 1 - D-GLYCERATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.29
	Engineered	:	YES
	Organism Scientific	:	HYPHOMICROBIUM METHYLOVORUM
	Organism Taxid	:	84

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:100 , VAL A:101 , THR A:102	BINDING SITE FOR RESIDUE SO4 A 322
2	AC2	SOFTWARE	HIS B:99 , GLY B:100 , VAL B:101 , THR B:102 , HOH B:354 , HOH B:376	BINDING SITE FOR RESIDUE SO4 B 322

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:269	-	Pro A:270
2	Glu B:269	-	Pro B:270

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	DHGY_HYPME	151-178	2	A:150-177 B:150-177
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	DHGY_HYPME	201-223	2	A:200-222 B:200-222
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	DHGY_HYPME	230-246	2	A:229-245 B:229-245

(no "Exon" information available for 1GDH)

Asymmetric/Biological 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:320
 aligned with DHGY_HYPME | P36234 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:320
                                    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
           DHGY_HYPME     3 KKKILITWPLPEAAMARARESYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASSSDEASYQATFHDSLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNTARGDLVDNELVVAALEAGRLAYAGFDVFAGEPNINEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYALA 322
               SCOP domains d1gdha2 A:2-100,A:292-321 D-glycerate dehydrogenase                                                d1gdha1 A:101-291 D-glycerate dehydrogenase                                                                                                                                                    d1gdha2 A:2-100,A:292-321      SCOP domains
               CATH domains 1gdhA01 A:2-101,A:291-318 NAD(P)-binding Rossmann-like Domain                                       1gdhA02 A:102-285 NAD(P)-binding Rossmann-like Domain                                                                                                                                   -----1gdhA01 A:2-101,A:291-318   --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhh.eeee........hhhhhhhh....eeeee......hhhhhh......eeeee........hhhhhh...eeee.....hhhhhhhhhhhhhhhh..hhhhhhhhh....................eeeee...hhhhhhhhhhhh...eeeee......hhhhhh..eee...hhhhhh...eeee.............hhhh......eeeee........hhhhhhhhhh..eeeeee..................eee........hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ----------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gdh A   2 KKKILITWPLPEAAMARARESYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASSSDEASYQATFHDSLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNTARGDLVDNELVVAALEAGRLAYAGFDVFAGEPNINEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYALA 321
                                    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

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with DHGY_HYPME | P36234 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:320
                                    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
           DHGY_HYPME     3 KKKILITWPLPEAAMARARESYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASSSDEASYQATFHDSLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNTARGDLVDNELVVAALEAGRLAYAGFDVFAGEPNINEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYALA 322
               SCOP domains d1gdhb2 B:2-100,B:292-321 D-glycerate dehydrogenase                                                d1gdhb1 B:101-291 D-glycerate dehydrogenase                                                                                                                                                    d1gdhb2 B:2-100,B:292-321      SCOP domains
               CATH domains 1gdhB01 B:2-101,B:291-318 NAD(P)-binding Rossmann-like Domain                                       1gdhB02 B:102-285 NAD(P)-binding Rossmann-like Domain                                                                                                                                   -----1gdhB01 B:2-101,B:291-318   --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhh.eeee........hhhhhhhh....eeeee......hhhhhh......eeeee........hhhhhh...eeee.....hhhhhhhhhhhhhhhh..hhhhhhhhh....................eeeee...hhhhhhhhhhhh...eeeee......hhhhhh..eee...hhhhhh...eeee.............hhhh......eeeee........hhhhhhhhhh..eeeeee..................eee........hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ----------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gdh B   2 KKKILITWPLPEAAMARARESYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASSSDEASYQATFHDSLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNTARGDLVDNELVVAALEAGRLAYAGFDVFAGEPNINEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYALA 321
                                    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

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Hyphomicrobium methylovorum. Organism_taxid: 84 (1)

1a	1gdhA02	A:102-285
1b	1gdhB02	B:102-285
1c	1gdhA01	A:2-101,A:291-318
1d	1gdhB01	B:2-101,B:291-318

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHGY_HYPME | P36234)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0008465	glycerate dehydrogenase activity	Catalysis of the reaction: (R)-glycerate + NAD+ = hydroxypyruvate + 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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:269 - Pro A:270	[ RasMol ]
		Glu B:269 - Pro B:270	[ RasMol ]

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	1gdh
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	DHGY_HYPME \| P36234
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	1.1.1.29
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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CATH Domains (1, 4)

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