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(-) Description

Title :  CRYSTAL STRUCTURES OF LEISHMANIA MEXICANA PHOSPHOGLYCERATE MUTASE AT HIGH COBALT CONCENTRATIONS
 
Authors :  M. W. Nowicki, B. Kuaprasert, I. W. Mcnae, H. P. Morgan, M. M. Harding, P. A. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
Date :  29 Jul 09  (Deposition) - 27 Oct 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  B
Keywords :  Glycolysis, Mutase, Cobalt, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Nowicki, B. Kuaprasert, I. W. Mcnae, H. P. Morgan, M. M. Harding, P. A. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw
Crystal Structures Of Leishmania Mexicana Phosphoglycerate Mutase Suggest A One-Metal Mechanism And A New Enzyme Subclass
J. Mol. Biol. V. 394 535 2009
PubMed-ID: 19781556  |  Reference-DOI: 10.1016/J.JMB.2009.09.041
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COFACTOR-INDEPENDENT PHOSPHOGLYCERATE MUTASE
    ChainsB
    EC Number5.4.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificLEISHMANIA MEXICANA
    Organism Taxid5665

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
12PG1Ligand/Ion2-PHOSPHOGLYCERIC ACID
23PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
3CO2Ligand/IonCOBALT (II) ION
4NA1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:425 , HIS B:429 , HIS B:496 , 3PG B:564 , 2PG B:565BINDING SITE FOR RESIDUE CO B 562
2AC2SOFTWAREASP B:23 , SER B:75 , LYS B:357 , ASP B:466 , HIS B:467 , 3PG B:564 , 2PG B:565BINDING SITE FOR RESIDUE CO B 563
3AC3SOFTWAREVAL B:36 , HIS B:37 , ALA B:39 , THR B:41 , HOH B:714 , HOH B:775BINDING SITE FOR RESIDUE NA B 601
4AC4SOFTWAREASP B:23 , ASN B:74 , SER B:75 , HIS B:136 , ARG B:166 , ASP B:167 , ARG B:202 , ARG B:209 , ARG B:282 , ARG B:285 , LYS B:357 , HIS B:360 , ASP B:425 , HIS B:429 , HIS B:467 , HIS B:496 , CO B:562 , CO B:563 , HOH B:593BINDING SITE FOR RESIDUE 3PG B 564
5AC5SOFTWAREASP B:23 , ASN B:74 , SER B:75 , HIS B:136 , ARG B:166 , ASP B:167 , ARG B:202 , ARG B:209 , ARG B:282 , ARG B:285 , LYS B:357 , HIS B:360 , ASP B:425 , HIS B:429 , HIS B:467 , HIS B:496 , CO B:562 , CO B:563 , HOH B:593BINDING SITE FOR RESIDUE 2PG B 565

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile B:323 -Pro B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IGY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IGY)

(-) Exons   (0, 0)

(no "Exon" information available for 3IGY)

(-) 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 B from PDB  Type:PROTEIN  Length:549
 aligned with Q86N96_LEIME | Q86N96 from UniProtKB/TrEMBL  Length:553

    Alignment length:549
                                    13        23        33        43        53        63        73        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       413       423       433       443       453       463       473       483       493       503       513       523       533       543         
         Q86N96_LEIME     4 LLLKPHKDLPRRTVLIVVMDGLGIGPEDDYDAVHMASTPFMDAHRRDNRHFRCVRAHGTAVGLPTDADMGNSEVGHNALGAGRVALQGASLVDDAIKSGEIYTGEGYRYLHGAFSKEGSTLHLIGLLSDGGVHSRDNQIYSIIEHAVKDGAKRIRVHALYDGRDVPDGSSFRFTDELEAVLAKVRQNGCDAAIASGGGRMFVTMDRYDADWSIVERGWRAQVLGDARHFHSAKEAITTFREEDPKVTDQYYPPFIVVDEQDKPLGTIEDGDAVLCVNFRGDRVIEMTRAFEDEDFNKFDRVRVPKVRYAGMMRYDGDLGIPNNFLVPPPKLTRVSEEYLCGSGLNIFACSETQKFGHVTYFWNGNRSGKIDEKHETFKEVPSDRVQFNEKPRMQSAAITEAAIEALKSGMYNVVRINFPNGDMVGHTGDLKATITGVEAVDESLAKLKDAVDSVNGVYIVTADHGNSDDMAQRDKKGKPMKDGNGNVLPLTSHTLSPVPVFIGGAGLDPRVAMRTDLPAAGLANVTATFINLLGFEAPEDYEPSLIYVE 552
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee...........hhhhhh.hhhhhhhhh....eeee..hhhhhh........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeeeeee...........hhhhhhhhhhhhh....eee.hhhhhhhhhhhhh..........eee...............eeee.......hhhhhhhhhh..............eeeeee...........eee.......hhhhhhhhh...eeeeeehhhhhhhh...............eeeeee.....hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....................................eeeeee.......eee.......hhhhhhhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igy B   4 LLLKPHKDLPRRTVLIVVMDGLGIGPEDDYDAVHMASTPFMDAHRRDNRHFRCVRAHGTAVGLPTDADMGNSEVGHNALGAGRVALQGASLVDDAIKSGEIYTGEGYRYLHGAFSKEGSTLHLIGLLSDGGVHSRDNQIYSIIEHAVKDGAKRIRVHALYDGRDVPDGSSFRFTDELEAVLAKVRQNGCDAAIASGGGRMFVTMDRYDADWSIVERGWRAQVLGDARHFHSAKEAITTFREEDPKVTDQYYPPFIVVDEQDKPLGTIEDGDAVLCVNFRGDRVIEMTRAFEDEDFNKFDRVRVPKVRYAGMMRYDGDLGIPNNFLVPPPKLTRVSEEYLCGSGLNIFACSETQKFGHVTYFWNGNRSGKIDEKHETFKEVPSDRVQFNEKPRMQSAAITEAAIEALKSGMYNVVRINFPNGDMVGHTGDLKATITGVEAVDESLAKLKDAVDSVNGVYIVTADHGNSDDMAQRDKKGKPMKDGNGNVLPLTSHTLSPVPVFIGGAGLDPRVAMRTDLPAAGLANVTATFINLLGFEAPEDYEPSLIYVE 552
                                    13        23        33        43        53        63        73        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       413       423       433       443       453       463       473       483       493       503       513       523       533       543         

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  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 3IGY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IGY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (Q86N96_LEIME | Q86N96)
molecular function
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004619    phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
biological process
    GO:0006007    glucose catabolic process    The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
    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.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q86N96_LEIME | Q86N963igz

(-) Related Entries Specified in the PDB File

1ejj CRYSTAL STRUCTURAL ANALYSIS OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COCRYSTALLIZED WITH 3- PHOSPHOGLYCERATE
1eqj CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE
3igz