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(-) Description

Title :  1.4A CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE
 
Authors :  D. J. Rigden, E. Lamani, J. E. Littlejohn, M. J. Jedrzejas
Date :  11 Dec 02  (Deposition) - 01 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Isomerase, Alpha/Beta-Type Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Rigden, L. V. Mello, E. Lamani, J. E. Littlejohn, M. J. Jedrzejas
Insights Into The Catalytic Mechanism Of Cofactor-Independent Phosphoglycerate Mutase From X-Ray Crystallography, Simulated Dynamics And Molecular Modeling
J. Mol. Biol. V. 328 909 2003
PubMed-ID: 12729763  |  Reference-DOI: 10.1016/S0022-2836(03)00350-4

(-) Compounds

Molecule 1 - 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
    Chains: A
    EC Number: 5.4.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGM:PUSH2
    Expression System Strain: M15
    Expression System Taxid: 562
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: PHOSPHOGLYCERATE MUTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
12PG1Ligand/Ion2-PHOSPHOGLYCERIC ACID
2MN2Ligand/IonMANGANESE (II) ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:403 , HIS A:407 , HIS A:462 , 2PG A:801BINDING SITE FOR RESIDUE MN A 601
2AC2SOFTWAREASP A:12 , SER A:62 , ASP A:444 , HIS A:445 , 2PG A:801BINDING SITE FOR RESIDUE MN A 701
3AC3SOFTWAREHIS A:297 , SER A:299 , GLU A:300 , PHE A:342 , GLU A:349 , HOH A:2462 , HOH A:2463BINDING SITE FOR RESIDUE SO4 A 901
4AC4SOFTWAREARG A:194 , ASP A:196 , ARG A:197 , HOH A:2230 , HOH A:2243 , HOH A:2464BINDING SITE FOR RESIDUE SO4 A 902
5AC5SOFTWAREARG A:17 , HOH A:2466 , HOH A:2467 , HOH A:2469BINDING SITE FOR RESIDUE SO4 A 903
6AC6SOFTWARETYR A:337 , GLU A:351 , ARG A:357 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473BINDING SITE FOR RESIDUE SO4 A 904
7AC7SOFTWAREARG A:134 , LYS A:170 , TYR A:174 , HOH A:2474BINDING SITE FOR RESIDUE SO4 A 905
8AC8SOFTWARELYS A:200 , ARG A:203 , TYR A:207 , GLY A:283 , PRO A:284 , HOH A:2249 , HOH A:2306BINDING SITE FOR RESIDUE SO4 A 906
9AC9SOFTWAREASN A:61 , SER A:62 , HIS A:123 , ARG A:153 , ASP A:154 , ARG A:185 , ARG A:191 , ARG A:261 , ARG A:264 , LYS A:336 , ASP A:403 , HIS A:407 , HIS A:462 , MN A:601 , MN A:701 , HOH A:2461BINDING SITE FOR RESIDUE 2PG A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O98)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O98)

(-) Exons   (0, 0)

(no "Exon" information available for 1O98)

(-) 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:509
 aligned with GPMI_GEOSE | Q9X519 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:509
                                    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       401       411       421       431       441       451       461       471       481       491       501         
           GPMI_GEOSE     2 SKKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNEYPHTTLKACGEAVGLPEGQMGNSEVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAAKEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDKRWDRVEKAYRAMVYGEGPTYRDPLECIEDSYKHGIYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFREFDRGPKHPKHLFFVCLTHFSETVKGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEKFPGEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKVVDAILAKGGIAIITADHGNADEVLTPDGKPQTAHTTNPVPVIVTKKGIKLRDGGILGDLAPTMLDLLGLPQPKEMTGKSLIV 510
               SCOP domains d1o98a2 A:2-76,A:311-510                                                   d1o98a1 A:77-310 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain                                                                                                                                    d1o98a2 A:2-76,A:311-510 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain                                                                                                   SCOP domains
               CATH domains -1o98A02 A:3-76,A:313-510 Alkaline Phosphatase, subunit A                  1o98A01 A:77-312 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain                                                                                                                                      1o98A02 A:3-76,A:313-510 Alkaline Phosphatase, subunit A                                                                                                                                               CATH domains
           Pfam domains (1) --Metalloenzyme-1o98A01 A:4-506                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------iPGM_N-1o98A02 A:82-308                                                                                                                                                                                                            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee...........hhhhhh.hhhhhhhhhhh.eeeee.hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeeehhhhh....hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhh..hhhhh..eee...............eeee.......hhhhhhhhhh................eeee..........ee.........hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhh....eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........................eeeee..........ee..hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o98 A   2 SKKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNEYPHTTLKACGEAVGLPEGQMGNSEVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAAKEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDKRWDRVEKAYRAMVYGEGPTYRDPLECIEDSYKHGIYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFREFDRGPKHPKHLFFVCLTHFSETVAGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEEFPGEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKVVDAILAKGGIAIITADHGNADEVLTPDGKPQTAHTTNPVPVIVTKKGIKLRDGGILGDLAPTMLDLLGLPQPKEMTGKSLIV 510
                                    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       401       411       421       431       441       451       461       471       481       491       501
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Alk_phosphatase (47)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GPMI_GEOSE | Q9X519)
molecular function
    GO:0046537    2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D glycerate; this reaction does not require the cofactor 2,3-bisphosphoglycerate.
    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: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:0043937    regulation of sporulation    Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
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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  1o98
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 Related Entries

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

UniProtKB/Swiss-Prot
        GPMI_GEOSE | Q9X519: 1ejj 1eqj 1o99

(-) Related Entries Specified in the PDB File

1ejj CRYSTAL STRUCTURAL ANALYSIS OF PHOSPHOGLYCERATE MUTASE COCRYSTALLIZED WITH 3-PHOSPHOGLYCERATE
1eqj CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE
1o99 CRYSTAL STRUCTURE OF THE S62A MUTANT OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE