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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPERM-SPECIFIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDS) COMPLEX WITH NAD AND PHOSPHATE
 
Authors :  A. Chaikuad, N. Shafqat, W. Yue, R. Cocking, J. E. Bray, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  30 Apr 09  (Deposition) - 26 May 09  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  O,P
Biol. Unit 1:  O,P  (2x)
Keywords :  Oxidoreductase, Structural Genomics, Structural Genomics Consortium, Sgc, Glycolysis, Nad, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, N. Shafqat, R. Al-Mokhtar, G. Cameron, A. R. Clarke, R. L. Brady, U. Oppermann, J. Frayne, W. W. Yue
Structure And Kinetic Characterization Of Human Sperm-Specific Glyceraldehyde-3-Phosphate Dehydrogenase, Gapds.
Biochem. J. V. 435 401 2011
PubMed-ID: 21269272  |  Reference-DOI: 10.1042/BJ20101442

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, TESTIS-SPECIFIC
    Chains: O, P
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CTHF
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 69-407
    Gene: GAPD2, GAPDH2, GAPDHS, GAPDS, HSD-35, HSD35
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPERMATOGENIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, SPERMATOGENIC CELL-SPECIFIC GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 2, GAPDH-2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 40)
No.NameCountTypeFull Name
1EDO28Ligand/Ion1,2-ETHANEDIOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO48Ligand/IonPHOSPHATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH O:27 , HOH O:32 , HOH O:56 , ASN O:81 , GLY O:82 , PHE O:83 , GLY O:84 , ARG O:85 , ILE O:86 , ASP O:106 , PRO O:107 , PHE O:108 , LYS O:151 , SER O:169 , THR O:170 , GLY O:171 , TYR O:173 , SER O:193 , ALA O:194 , ALA O:255 , ASN O:388 , TYR O:392 , PO4 O:415 , HOH O:424 , HOH O:439 , HOH O:448 , HOH O:456 , HOH O:459 , HOH O:465 , HOH O:472 , HOH O:559 , HOH O:563 , HOH O:569 , HOH O:571 , HOH O:579 , HOH O:602BINDING SITE FOR RESIDUE NAD O 2
02AC2SOFTWARENAD O:2 , THR O:254 , THR O:256 , ARG O:306 , HOH O:424 , HOH O:455 , HOH O:468 , HOH O:492 , HOH O:532 , HOH O:559 , HOH O:595BINDING SITE FOR RESIDUE PO4 O 415
03AC3SOFTWAREHOH O:37 , SER O:223 , CYS O:224 , THR O:225 , HIS O:251 , THR O:283 , GLY O:284 , HOH O:424 , HOH O:455 , HOH O:564 , HOH O:595BINDING SITE FOR RESIDUE PO4 O 4
04AC4SOFTWAREALA O:267 , TRP O:268 , HOH O:527BINDING SITE FOR RESIDUE EDO O 8
05AC5SOFTWAREPRO O:200 , MET O:201 , ASN O:207 , LYS O:291 , HOH O:577BINDING SITE FOR RESIDUE EDO O 9
06AC6SOFTWAREGLU O:244 , ARG O:320 , HOH O:600 , ARG P:320 , ASN P:376 , ASN P:378 , HOH P:618BINDING SITE FOR RESIDUE EDO O 14
07AC7SOFTWAREGLY O:205 , ASN O:207 , GLU O:208 , ASN O:209 , HOH O:567BINDING SITE FOR RESIDUE EDO O 15
08AC8SOFTWARELYS O:331BINDING SITE FOR RESIDUE EDO O 17
09AC9SOFTWAREARG O:269 , GLU P:352 , LYS P:370 , HOH P:502BINDING SITE FOR RESIDUE EDO O 18
10BC1SOFTWAREHOH P:19 , HOH P:28 , HOH P:55 , HOH P:60 , HOH P:62 , ASN P:81 , GLY P:82 , PHE P:83 , GLY P:84 , ARG P:85 , ILE P:86 , ASP P:106 , PRO P:107 , PHE P:108 , LYS P:151 , SER P:169 , THR P:170 , GLY P:171 , TYR P:173 , SER P:193 , ALA P:194 , ALA P:255 , PRO P:263 , ASN P:388 , TYR P:392 , PO4 P:415 , HOH P:489 , HOH P:511 , HOH P:531 , HOH P:545 , HOH P:549 , HOH P:586 , HOH P:596 , HOH P:607 , HOH P:608 , HOH P:609BINDING SITE FOR RESIDUE NAD P 1
11BC2SOFTWARENAD P:1 , HOH P:60 , THR P:254 , THR P:256 , ARG P:306 , HOH P:434 , HOH P:436 , HOH P:510 , HOH P:549 , HOH P:581 , HOH P:622BINDING SITE FOR RESIDUE PO4 P 415
12BC3SOFTWARESER P:223 , CYS P:224 , THR P:225 , HIS P:251 , THR P:283 , GLY P:284 , ARG P:306 , HOH P:436 , HOH P:495 , HOH P:549 , HOH P:614 , HOH P:622BINDING SITE FOR RESIDUE PO4 P 3
13BC4SOFTWAREARG O:126 , HOH O:506 , PHE P:358 , ASP P:361BINDING SITE FOR RESIDUE EDO P 5
14BC5SOFTWAREALA P:267 , TRP P:268 , HOH P:620BINDING SITE FOR RESIDUE EDO P 6
15BC6SOFTWAREPRO P:200 , MET P:201 , ASN P:207 , HOH P:593 , HOH P:625BINDING SITE FOR RESIDUE EDO P 7
16BC7SOFTWAREVAL P:206 , ASN P:207 , GLU P:208 , ASN P:209BINDING SITE FOR RESIDUE EDO P 10
17BC8SOFTWAREPHE O:358 , ASP O:361 , ARG P:126 , HOH P:494BINDING SITE FOR RESIDUE EDO P 11
18BC9SOFTWAREEDO P:13 , ALA P:369 , GLY P:372 , HOH P:616BINDING SITE FOR RESIDUE EDO P 12
19CC1SOFTWAREEDO P:12 , LYS P:331 , LYS P:370BINDING SITE FOR RESIDUE EDO P 13
20CC2SOFTWAREPRO P:197 , LYS P:291 , PRO P:324 , PRO P:326 , ASP P:377 , HOH P:593BINDING SITE FOR RESIDUE EDO P 16

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H9E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H9E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049219D110NG3PT_HUMANPolymorphism2285514O/PD110N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049219D110NG3PT_HUMANPolymorphism2285514O/PD110N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3PT_HUMAN222-229
 		  2O:222-229
P:222-229
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3PT_HUMAN222-229
 		  4O:222-229
P:222-229

(-) Exons   (0, 0)

(no "Exon" information available for 3H9E)

(-) 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:336
 aligned with G3PT_HUMAN | O14556 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:336
                                                                                                                                                                                                                                                                                                                                                                        408 
                                    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    | 
           G3PT_HUMAN    74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNASCTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDK-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh......eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee..............hhhhhh......eee..hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------N----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h9e O  74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNASCTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDAE 409
                                    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      


Chain P from PDB  Type:PROTEIN  Length:337
 aligned with G3PT_HUMAN | O14556 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:337
                                                                                                                                                                                                                                                                                                                                                                        408  
                                    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    |  
           G3PT_HUMAN    74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNASCTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDK--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh......eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee..............hhhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------N------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h9e P  74 RELTVGINGFGRIGRLVLRACMEKGVKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGSVEFRNGQLVVDNHEISVYQCKEPKQIPWRAVGSPYVVESTGVYLSIQAASDHISAGAQRVVISAPSPDAPMFVMGVNENDYNPGSMNIVSNASCTTNCLAPLAKVIHERFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPASTGAAKAVTKVIPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPAPYSAIKEAVKAAAKGPMAGILAYTEDEVVSTDFLGDTHSSIFDAKAGIALNDNFVKLISWYDNEYGYSHRVVDLLRYMFSRDAEN 410
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3H9E)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H9E)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain O,P   (G3PT_HUMAN | O14556)
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:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + 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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0061621    canonical glycolysis    The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
    GO:0030317    flagellated sperm motility    Any process involved in the controlled movement of a flagellated sperm cell.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    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:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.
    GO:0045821    positive regulation of glycolytic process    Any process that activates or increases the frequency, rate or extent of glycolysis.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3h9e
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  G3PT_HUMAN | O14556
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  1.2.1.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        G3PT_HUMAN | O14556: 3pfw 5c7l 5c7o

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3H9E)