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(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF PHOSPHOGLYCERATE KINASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA
 
Authors :  G. Auerbach, R. Huber, M. Graettinger, K. Zaiss, H. Schurig, R. Jaenicke, U. Jacob
Date :  06 May 97  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Phosphoglycerate Kinase, Thermotoga Maritima, Hyperthermostability, Crystal, Amp-Pnp, 3-Pga (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Auerbach, R. Huber, M. Grattinger, K. Zaiss, H. Schurig, R. Jaenicke, U. Jacob
Closed Structure Of Phosphoglycerate Kinase From Thermotoga Maritima Reveals The Catalytic Mechanism And Determinants Of Thermal Stability.
Structure V. 5 1475 1997
PubMed-ID: 9384563  |  Reference-DOI: 10.1016/S0969-2126(97)00297-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE KINASE
    ChainsA
    EC Number2.7.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOSOL
    Expression System Taxid562
    Expression System Vector TypeBACTERIUM
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREANP A:400 , HOH A:626 , HOH A:627 , HOH A:628BINDING SITE FOR RESIDUE MG A 402
2AC2SOFTWAREGLY A:195 , ALA A:196 , LYS A:197 , LYS A:201 , GLY A:219 , ALA A:220 , GLY A:293 , ASN A:317 , PRO A:319 , GLY A:321 , VAL A:322 , GLU A:324 , GLY A:353 , GLY A:354 , ASP A:355 , SER A:356 , THR A:374 , GLY A:376 , MG A:402 , HOH A:427 , HOH A:518 , HOH A:585 , HOH A:626 , HOH A:627 , HOH A:628BINDING SITE FOR RESIDUE ANP A 400
3AC3SOFTWAREASP A:21 , ASN A:23 , ARG A:36 , HIS A:59 , ARG A:62 , ARG A:118 , GLY A:147 , ARG A:151 , HOH A:422 , HOH A:452 , HOH A:459 , HOH A:475 , HOH A:585BINDING SITE FOR RESIDUE 3PG A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGKT_THEMA15-25  1A:15-25

(-) Exons   (0, 0)

(no "Exon" information available for 1VPE)

(-) 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:398
 aligned with PGKT_THEMA | P36204 from UniProtKB/Swiss-Prot  Length:654

    Alignment length:398
                                    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        
           PGKT_THEMA     2 EKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399
               SCOP domains d1vpea_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1vpeA01 A:2-170  [code=3.40.50.1260, no name defined]                                                                                                                    ------1vpeA02 A:177-384  [code=3.40.50.1270, no name defined]                                                                                                                                                         --------------- CATH domains
               Pfam domains ---PGK-1vpeA01 A:5-386                                                                                                                                                                                                                                                                                                                                                                           ------------- Pfam domains
         Sec.struct. author ....hhh......eeeee...............hhhhhhhhhhhhhhh...eeeee...........hhh..hhhhhhhhhhh....eee.....hhhhhhhh.....eeeee..hhh..hhhh..hhhhhhhhhh..eeee..hhh.........hhhh..eeee.hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeee...hhhhhhhhh..........hhhhhhhhhhhhhhhh...eee...eeeee.........eeee.........eeeee.hhhhhhhhhhh....eeeee........hhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhh...hhh..eee..hhhhhhhhh....hhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpe A   2 EKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKELVEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASMRIKKA 399
                                    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        

   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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGKT_THEMA | P36204)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
    GO:0004807    triose-phosphate isomerase activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    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:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
    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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