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(-) Description

Title :  ENZYME-LIGAND COMPLEX OF P. AERUGINOSA PMM/PGM
 
Authors :  C. Regni, P. A. Tipton, L. J. Beamer
Date :  16 May 03  (Deposition) - 20 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  X
Keywords :  Alpha/Beta Protein, Phosphohexomutase, Phosphoserine, Enzyme-Ligand Complex, Enzyme-Metal Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Regni, L. Naught, P. A. Tipton, L. J. Beamer
Structural Basis Of Diverse Substrate Recognition By The Enzyme Pmm/Pgm From P. Aeruginosa.
Structure V. 12 55 2004
PubMed-ID: 14725765  |  Reference-DOI: 10.1016/J.STR.2003.11.015

(-) Compounds

Molecule 1 - PHOSPHOMANNOMUTASE
    ChainsX
    EC Number5.4.2.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3-A
    Expression System StrainB121(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneALGC OR PA5322
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    SynonymPMM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1M6P1Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESEP X:108 , ASP X:242 , ASP X:244 , ASP X:246BINDING SITE FOR RESIDUE ZN X 500
2AC2SOFTWARETYR X:17 , SEP X:108 , LYS X:285 , THR X:306 , GLY X:307 , HIS X:308 , GLU X:325 , SER X:327 , HIS X:329 , ARG X:421 , SER X:423 , ASN X:424 , THR X:425 , HOH X:636 , HOH X:715 , HOH X:813BINDING SITE FOR RESIDUE M6P X 600

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1X:179 -X:204

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGM_PMMPS00710 Phosphoglucomutase and phosphomannomutase phosphoserine signature.ALGC_PSEAE102-111  1X:102-111

(-) Exons   (0, 0)

(no "Exon" information available for 1PCM)

(-) 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 X from PDB  Type:PROTEIN  Length:455
 aligned with ALGC_PSEAE | P26276 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:455
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458     
           ALGC_PSEAE     9 LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
               SCOP domains d1pcmx1 X:9-154 Phosphomannomutase/phosphoglucomutase                                                                                             d1pcmx2 X:155-258 Phosphomannomutase/phosphoglucomutase                                                 d1pcmx3 X:259-367 Phosphomannomutase/phosphoglucomutase                                                      d1pcmx4 X:368-463 Phosphomannomutase/phosphoglucomutase                                          SCOP domains
               CATH domains 1pcmX01 X:9-154 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                                             -------------------1pcmX02 X:174-251 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3       1pcmX03 X:252-370 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                1pcmX04 X:371-463 Major birch pollen allergen Bet v 1                                         CATH domains
               Pfam domains --PGM_PMM_I-1pcmX04 X:11-145                                                                                                             -----------PGM_PMM_II-1pcmX02 X:157-255                                                                       ---PGM_PMM_III-1pcmX01 X:259-370                                                                                   ----PGM_PMM_IV-1pcmX03 X:375-453                                                   ---------- Pfam domains
         Sec.struct. author .hhhhh....eeee.....hhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh...eeeee........eeeeeeee..ee..hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhh.eeeeee................hhhhhhhhhhhhhhh...eeeee......eeeee....eehhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh..eeeee..hhhhhhhhhhhhh..eee.....eee........hhhhhhhhhhhhhhh...hhhhhhhh....ee...eeee....hhhhhhhhhhhhh.....eee....eeeee..eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------PGM_PMM   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pcm X   9 LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGsHNPPDYNGFKIVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458     
                                                                                                                             108-SEP                                                                                                                                                                                                                                                                                                                                                               

   Legend:   → Mismatch (orange background)
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  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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (ALGC_PSEAE | P26276)
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: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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004614    phosphoglucomutase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.
    GO:0004615    phosphomannomutase activity    Catalysis of the reaction: alpha-D-mannose 1-phosphate = D-mannose 6-phosphate.
biological process
    GO:0009298    GDP-mannose biosynthetic process    The chemical reactions and pathways resulting in the formation of GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
    GO:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    GO:0042121    alginic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
    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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0009244    lipopolysaccharide core region biosynthetic process    The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
    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:0071704    organic substance metabolic process    The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALGC_PSEAE | P262761k2y 1k35 1p5d 1p5g 1pcj 2fkf 2fkm 2h4l 2h5a 3bkq 3c04 3rsm 4il8 4mrq

(-) Related Entries Specified in the PDB File

1k2y S108A MUTANT OF PMM/PGM
1k35 APO PMM/PGM STRUCTURE
1p5d PMM/PGM WITH D-GLUCOSE 1-PHOSPHATE BOUND
1p5g PMM/PGM WITH D-GLUCOSE 6-PHOSPHATE BOUND
1pcj PMM/PGM WITH D-MANNOSE 1-PHOSPHATE BOUND