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(-) Description

Title :  STRUCTURE OF THE ADP COMPLEX OF THE 3-PHOSPHOGLYCERATE KINASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.65 ANGSTROMS
 
Authors :  G. J. Davies, H. C. Watson
Date :  12 Apr 94  (Deposition) - 22 Jun 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Davies, S. J. Gamblin, J. A. Littlechild, Z. Dauter, K. S. Wilson, H. C. Watson
Structure Of The Adp Complex Of The 3-Phosphoglycerate Kinase From Bacillus Stearothermophilus At 1. 65 A.
Acta Crystallogr. , Sect. D V. 50 202 1994
PubMed-ID: 15299460  |  Reference-DOI: 10.1107/S0907444993011138
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-PHOSPHOGLYCERATE KINASE
    Chains: A
    EC Number: 2.7.2.3
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:352 , ADP A:396 , HOH A:1021 , HOH A:1022 , HOH A:1023BINDING SITE FOR RESIDUE MG A 395
2AC2SOFTWAREGLY A:195 , ALA A:196 , LYS A:201 , GLY A:219 , GLY A:220 , LEU A:237 , ALA A:292 , LEU A:293 , ASN A:316 , PRO A:318 , GLY A:320 , VAL A:321 , GLU A:323 , GLY A:350 , GLY A:351 , ASP A:352 , SER A:353 , MG A:395 , HOH A:458 , HOH A:465 , HOH A:477 , HOH A:1021 , HOH A:1022 , HOH A:1024 , HOH A:1025BINDING SITE FOR RESIDUE ADP A 396

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:187 -Pro A:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_GEOSE15-25  1A:15-25

(-) Exons   (0, 0)

(no "Exon" information available for 1PHP)

(-) Sequences/Alignments

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:394
 aligned with PGK_GEOSE | P18912 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    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    
            PGK_GEOSE     1 MNKKTIRDVDVRGKRVFCRVDFNVPMEQGAITDDTRIRAALPTIRYLIEHGAKVILASHLGRPKGKVVEELRLDAVAKRLGELLERPVAKTNEAVGDEVKAAVDRLNEGDVLLLENVRFYPGEEKNDPELAKAFAELADLYVNDAFGAAHRAHASTEGIAHYLPAVAGFLMEKELEVLGKALSNPDRPFTAIIGGAKVKDKIGVIDNLLEKVDNLIIGGGLAYTFVKALGHDVGKSLLEEDKIELAKSFMEKAKEKGVRFYMPVDVVVADRFANDANTKVVPIDAIPADWSALDIGPKTRELYRDVIRESKLVVWNGPMGVFEMDAFAHGTKAIAEALAEALDTYSVIGGGDSAAAVEKFGLADKMDHISTGGGASLEFMEGKQLPGVVALEDK 394
               SCOP domains d1phpa_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1phpA01 A:1-170  [code=3.40.50.1260, no name defined]                                                                                                                     ------1phpA02 A:177-381  [code=3.40.50.1270, no name defined]                                                                                                                                                      ------------- CATH domains
               Pfam domains ----PGK-1phpA01 A:5-383                                                                                                                                                                                                                                                                                                                                                                        ----------- Pfam domains
         Sec.struct. author .....hhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhh...eeee.hhhhh.......hhhhhh..eeehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.eee...eeeee........eeeee.hhh....eeeeehhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.hhhhh.ee...hhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PGLYCERATE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1php A   1 MNKKTIRDVDVRGKRVFCRVDFNVPMEQGAITDDTRIRAALPTIRYLIEHGAKVILASHLGRPKGKVVEELRLDAVAKRLGELLERPVAKTNEAVGDEVKAAVDRLNEGDVLLLENVRFYPGEEKNDPELAKAFAELADLYVNDAFGAAHRAHASTEGIAHYLPAVAGFLMEKELEVLGKALSNPDRPFTAIIGGAKVKDKIGVIDNLLEKVDNLIIGGGLAYTFVKALGHDVGKSLLEEDKIELAKSFMEKAKEKGVRFYMPVDVVVADRFANDANTKVVPIDAIPADWSALDIGPKTRELYRDVIRESKLVVWNGPMGVFEMDAFAHGTKAIAEALAEALDTYSVIGGGDSAAAVEKFGLADKMDHISTGGGASLEFMEGKQLPGVVALEDK 394
                                    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
   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  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PGK] (23)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGK_GEOSE | P18912)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004618    phosphoglycerate kinase activity    Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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