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(-) Description

Title :  CRYSTAL STRUCTURE OF BISPHOSPHOGLYCERATE MUTASE IN COMPLEX WITH 3-PHOSPHOGLYCERATE AND ALF4-
 
Authors :  Y. Wang, L. Liu, Z. Wei, W. Gong
Date :  05 Dec 05  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bisphosphoglycerate Mutase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Wang, L. Liu, Z. Wei, Z. Cheng, Y. Lin, W. Gong
Seeing The Process Of Histidine Phosphorylation In Human Bisphosphoglycerate Mutase
J. Biol. Chem. V. 281 39642 2006
PubMed-ID: 17052986  |  Reference-DOI: 10.1074/JBC.M606421200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BISPHOSPHOGLYCERATE MUTASE
    ChainsA, B
    EC Number5.4.2.4, 5.4.2.1, 3.1.3.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym2,3-BISPHOSPHOGLYCERATE MUTASE, ERYTHROCYTE, 2,3- BISPHOSPHOGLYCERATE SYNTHASE, BPGM, BPG-DEPENDENT PGAM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2ALF2Ligand/IonTETRAFLUOROALUMINATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , HIS A:11 , ASN A:17 , GLN A:28 , ARG A:62 , GLU A:89 , HIS A:188 , GLY A:189 , 3PG A:408 , HOH A:588BINDING SITE FOR RESIDUE ALF A 400
2AC2SOFTWAREARG B:10 , HIS B:11 , ASN B:17 , ARG B:62 , GLU B:89 , HIS B:188 , GLY B:189 , 3PG B:409 , HOH B:601BINDING SITE FOR RESIDUE ALF B 401
3AC3SOFTWAREARG A:10 , PHE A:22 , CYS A:23 , SER A:24 , GLU A:89 , TYR A:92 , ARG A:100 , ARG A:116 , ARG A:117 , ASN A:190 , ALF A:400 , HOH A:438 , HOH A:448 , HOH A:518BINDING SITE FOR RESIDUE 3PG A 408
4AC4SOFTWAREPHE B:22 , CYS B:23 , SER B:24 , GLU B:89 , TYR B:92 , ARG B:100 , ARG B:116 , ARG B:117 , ASN B:190 , ALF B:401 , HOH B:415 , HOH B:442 , HOH B:449BINDING SITE FOR RESIDUE 3PG B 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065367R62QPMGE_HUMANDisease (BPGMD)751972865A/BR62Q
2UniProtVAR_065368R90CPMGE_HUMANDisease (BPGMD)121964925A/BR90C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.PMGE_HUMAN8-17
 
  2A:8-17
B:8-17

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003931321cENSE00001895644chr7:134331583-134331689107PMGE_HUMAN-00--
1.3ENST000003931323ENSE00001514256chr7:134343100-134343420321PMGE_HUMAN-00--
1.5bENST000003931325bENSE00001242893chr7:134346199-134346860662PMGE_HUMAN1-2012012A:3-201
B:3-201
199
199
1.6bENST000003931326bENSE00001372027chr7:134363605-134364565961PMGE_HUMAN201-259592A:201-256
B:201-255
56
55

(-) 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:254
 aligned with PMGE_HUMAN | P07738 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    
           PMGE_HUMAN     3 KYKLIMLRHGEGAWNKENRFCSWVDQKLNSEGMEEARNCGKQLKALNFEFDLVFTSVLNRSIHTAWLILEELGQEWVPVESSWRLNERHYGALIGLNREQMALNHGEEQVRLWRRSYNVTPPPIEESHPYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGNSSRALLKHLEGISDEDIINITLPTGVPILLELDENLRAVGPHQFLGDQEAIQAAIKKVEDQGKVKQ 256
               SCOP domains d2f90a_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2f90A00 A:3-256 Phosphoglycerate mutase-like                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh...hhhhhh.......eeeee..........ee..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------Q---------------------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: A:3-201 UniProt: 1-201 [INCOMPLETE]                                                                                                                                                    ------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6b  PDB: A:201-256 UniProt: 201-259 [INCOMPLETE]  Transcript 1 (2)
                 2f90 A   3 KYKLIMLRHGEGAWNKENRFCSWVDQKLNSEGMEEARNCGKQLKALNFEFDLVFTSVLNRSIHTAWLILEELGQEWVPVESSWRLNERHYGALIGLNREQMALNHGEEQVRLWRRSYNVTPPPIEESHPYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGNSSRALLKHLEGISDEDIINITLPTGVPILLELDENLRAVGPHQFLGDQEAIQAAIKKVEDQGKVKQ 256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with PMGE_HUMAN | P07738 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   
           PMGE_HUMAN     3 KYKLIMLRHGEGAWNKENRFCSWVDQKLNSEGMEEARNCGKQLKALNFEFDLVFTSVLNRSIHTAWLILEELGQEWVPVESSWRLNERHYGALIGLNREQMALNHGEEQVRLWRRSYNVTPPPIEESHPYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGNSSRALLKHLEGISDEDIINITLPTGVPILLELDENLRAVGPHQFLGDQEAIQAAIKKVEDQGKVK 255
               SCOP domains d2f90b_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2f90B00 B:3-255 Phosphoglycerate mutase-like                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh...hhhhhh.......eeeee..........ee..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------Q---------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: B:3-201 UniProt: 1-201 [INCOMPLETE]                                                                                                                                                    ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6b  PDB: B:201-255 UniProt: 201-259 [INCOMPLETE] Transcript 1 (2)
                 2f90 B   3 KYKLIMLRHGEGAWNKENRFCSWVDQKLNSEGMEEARNCGKQLKALNFEFDLVFTSVLNRSIHTAWLILEELGQEWVPVESSWRLNERHYGALIGLNREQMALNHGEEQVRLWRRSYNVTPPPIEESHPYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGNSSRALLKHLEGISDEDIINITLPTGVPILLELDENLRAVGPHQFLGDQEAIQAAIKKVEDQGKVK 255
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F90)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PMGE_HUMAN | P07738)
molecular function
    GO:0046538    2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction requires the cofactor 2,3-bisphosphoglycerate.
    GO:0004083    bisphosphoglycerate 2-phosphatase activity    Catalysis of the reaction: 2,3-bisphospho-D-glycerate + H(2)O = 3-phospho-D-glycerate + phosphate.
    GO:0004082    bisphosphoglycerate mutase activity    Catalysis of the reaction: 3-phospho-D-glyceroyl phosphate = 2,3-bisphospho-D-glycerate.
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016868    intramolecular transferase activity, phosphotransferases    Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
    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:0004619    phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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: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:0043456    regulation of pentose-phosphate shunt    Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
cellular component
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PMGE_HUMAN | P077381t8p 2a9j 2h4x 2h4z 2h52 2hhj 3nfy

(-) Related Entries Specified in the PDB File

1t8p THE SAME PROTEIN COMPLEXED WITH NO LIGAND.