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(-) Description

Title :  THE CRYSTAL STRUCTURE OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ALCALIGENES XYLOSOXIDANS AT 1.7 A RESOLUTION.
 
Authors :  S. V. Antonyuk, R. R. Eady, R. W. Strange, S. S. Hasnain
Date :  30 Jan 03  (Deposition) - 12 Jun 03  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  O,P
Biol. Unit 1:  O,P  (2x)
Keywords :  Glycolytic Pathway, Oxidoreductase, Free-Nad Gapdh (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, R. R. Eady, R. W. Strange, S. S. Hasnain
The Structure Of Glyceraldehyde 3-Phosphate Dehydrogenase From Alcaligenes Xylosoxidans At 1. 7 A Resolution
Acta Crystallogr. , Sect. D V. 59 835 2003
PubMed-ID: 12777799  |  Reference-DOI: 10.1107/S0907444903041441

(-) Compounds

Molecule 1 - GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
    Chains: O, P
    EC Number: 1.2.1.12
    Organism Common: ALCALIGENES XYLOSOXIDANS
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : OP
Biological Unit 1 (2x): OP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2K2Ligand/IonPOTASSIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CSD4Mod. Amino Acid3-SULFINOALANINE
2K-1Ligand/IonPOTASSIUM ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR O:184 , ASN O:186 , ARG O:199 , ARG O:235 , HOH O:2245BINDING SITE FOR RESIDUE SO4 O 341
2AC2SOFTWARESER O:153 , THR O:212 , GLY O:213 , ALA O:214 , HOH O:2246 , HOH O:2247BINDING SITE FOR RESIDUE SO4 O 342
3AC3SOFTWAREASN O:185 , ASN O:186 , GLN O:187BINDING SITE FOR RESIDUE K O 343
4AC4SOFTWARETHR P:184 , ARG P:199 , ARG P:235 , HOH P:2252BINDING SITE FOR RESIDUE SO4 P 341
5AC5SOFTWAREASN P:185 , ASN P:186 , GLN P:187 , PG4 P:344 , HOH P:2253BINDING SITE FOR RESIDUE K P 343
6AC6SOFTWAREASN P:185 , ASN P:186 , VAL P:188 , TYR P:193 , K P:343 , HOH P:2133 , HOH P:2253 , HOH P:2254 , HOH P:2255BINDING SITE FOR RESIDUE PG4 P 344

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OBF)

(-) Exons   (0, 0)

(no "Exon" information available for 1OBF)

(-) 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 O from PDB  Type:PROTEIN  Length:335
 aligned with P83696_ALCXX | P83696 from UniProtKB/TrEMBL  Length:335

    Alignment length:335
                                    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     
         P83696_ALCXX     1 TIRVAINGYGRIGRNILRAHYEGGKSHDIEIVAINDLGDPKTNAHLTRYDTAHGKFPGTVSVNGSYMVVNGDKIRVDANRNPAQLPWGALKVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGADVDATVVYGVNHGTLKSTDTVISNASCTTNCLAPLVKPLNDKLGLQDGLMTTVHAYTNNQVLTDVYHEDLRRARSATMSMIPTKTGAAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAASEGELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNEWGFSNRMLDTTVALMSAA 335
               SCOP domains d1obfo1 O:1-152,O:315-335 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                              d1obfo2 O:153-314 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                d1obfo1               SCOP domains
               CATH domains 1obfO01 O:1-152,O:317-334 NAD(P)-binding Rossmann-like Domain                                                                                           1obfO02 O:153-316 Dihydrodipicolinate Reductase; domain 2                                                                                                           1obfO01           - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhee...ee....eeee..eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhhh..eeee.........ee.....hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.........................eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee..eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obf O   1 TIRVAINGYGRIGRNILRAHYEGGKSHDIEIVAINDLGDPKTNAHLTRYDTAHGKFPGTVSVNGSYMVVNGDKIRVDANRNPAQLPWGALKVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGADVDATVVYGVNHGTLKSTDTVISNAScTTNCLAPLVKPLNDKLGLQDGLMTTVHAYTNNQVLTDVYHEDLRRARSATMSMIPTKTGAAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAASEGELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNEWGFSNRMLDTTVALMSAA 335
                                    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     
                                                                                                                                                                                   154-CSD                                                                                                                                                                                 


Chain P from PDB  Type:PROTEIN  Length:335
 aligned with P83696_ALCXX | P83696 from UniProtKB/TrEMBL  Length:335

    Alignment length:335
                                    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     
         P83696_ALCXX     1 TIRVAINGYGRIGRNILRAHYEGGKSHDIEIVAINDLGDPKTNAHLTRYDTAHGKFPGTVSVNGSYMVVNGDKIRVDANRNPAQLPWGALKVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGADVDATVVYGVNHGTLKSTDTVISNASCTTNCLAPLVKPLNDKLGLQDGLMTTVHAYTNNQVLTDVYHEDLRRARSATMSMIPTKTGAAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAASEGELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNEWGFSNRMLDTTVALMSAA 335
               SCOP domains d1obfp1 P:1-152,P:315-335 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                              d1obfp2 P:153-314 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                d1obfp1               SCOP domains
               CATH domains 1obfP01 P:1-152,P:317-334 NAD(P)-binding Rossmann-like Domain                                                                                           1obfP02 P:153-316 Dihydrodipicolinate Reductase; domain 2                                                                                                           1obfP01           - CATH domains
           Pfam domains (1) -Gp_dh_N-1obfP03 P:2-154                                                                                                                                  ----Gp_dh_C-1obfP01 P:159-314                                                                                                                                   --------------------- Pfam domains (1)
           Pfam domains (2) -Gp_dh_N-1obfP04 P:2-154                                                                                                                                  ----Gp_dh_C-1obfP02 P:159-314                                                                                                                                   --------------------- Pfam domains (2)
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee................hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.........................eee......hhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee..eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obf P   1 TIRVAINGYGRIGRNILRAHYEGGKSHDIEIVAINDLGDPKTNAHLTRYDTAHGKFPGTVSVNGSYMVVNGDKIRVDANRNPAQLPWGALKVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGADVDATVVYGVNHGTLKSTDTVISNAScTTNCLAPLVKPLNDKLGLQDGLMTTVHAYTNNQVLTDVYHEDLRRARSATMSMIPTKTGAAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAASEGELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNEWGFSNRMLDTTVALMSAA 335
                                    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     
                                                                                                                                                                                   154-CSD
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GADPH_aa-bio_dh (59)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain O,P   (P83696_ALCXX | P83696)
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:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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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