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(-) Description

Title :  CRYSTAL STRUCTURE OF MANNOSE 6-PHOSPHATE ISOMERASE (APO FORM) FROM SALMONELLA TYPHIMURIUM
 
Authors :  S. R. Sagurthi
Date :  13 Apr 09  (Deposition) - 14 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Isomerase, Apo-Structure, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Sagurthi, G. Gowda, H. S. Savithri, M. R. N. Murthy
Crystal Structures Of Mannose 6-Phosphate Isomerase From Salmonella Typhimurium Bound To Metal Atoms And Substrate: Implications For Catalytic Mechanism
Acta Crystallogr. , Sect. D V. 65 724 2009
PubMed-ID: 19564693  |  Reference-DOI: 10.1107/S0907444909013328

(-) Compounds

Molecule 1 - MANNOSE-6-PHOSPHATE ISOMERASE
    Atcc: 9150
    Chains: A
    EC Number: 5.3.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETC
    Expression System Strain: PLYSIS
    Expression System Taxid: 562
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: MANNOSE 6-PHOSPHATE ISOMERASE, PHOSPHOMANNOSE ISOMERASE, PMI, PHOSPHOHEXOMUTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric/Biological Unit (1, 16)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:353 , LYS A:354 , ASP A:355 , PRO A:375 , ASN A:377 , HOH A:2359BINDING SITE FOR RESIDUE EDO A1392
02AC2SOFTWARELYS A:195 , ASP A:227 , SER A:228 , THR A:278 , EDO A:1403 , HOH A:2262 , HOH A:2360BINDING SITE FOR RESIDUE EDO A1393
03AC3SOFTWARESER A:95 , GLN A:97 , HOH A:2106BINDING SITE FOR RESIDUE EDO A1394
04AC4SOFTWAREILE A:96 , PHE A:184 , SER A:228 , GLY A:229 , PHE A:231 , SER A:232 , ALA A:275BINDING SITE FOR RESIDUE EDO A1395
05AC5SOFTWAREASN A:6 , LYS A:307 , SER A:308 , GLY A:309 , EDO A:1400 , HOH A:2364BINDING SITE FOR RESIDUE EDO A1396
06AC6SOFTWAREALA A:185 , ASN A:189 , ILE A:284BINDING SITE FOR RESIDUE EDO A1397
07AC7SOFTWAREARG A:77 , VAL A:155 , LEU A:172 , PRO A:175 , EDO A:1405 , HOH A:2361 , HOH A:2362BINDING SITE FOR RESIDUE EDO A1398
08AC8SOFTWAREHOH A:2363BINDING SITE FOR RESIDUE EDO A1399
09AC9SOFTWAREASN A:6 , GLY A:364 , EDO A:1396 , HOH A:2014 , HOH A:2364BINDING SITE FOR RESIDUE EDO A1400
10BC1SOFTWAREALA A:310 , GLU A:311 , HIS A:326 , SER A:334 , HOH A:2315 , HOH A:2365BINDING SITE FOR RESIDUE EDO A1401
11BC2SOFTWAREASN A:104 , LYS A:111 , TYR A:126 , GLU A:286 , ASN A:290 , HOH A:2366BINDING SITE FOR RESIDUE EDO A1402
12BC3SOFTWAREMET A:190 , GLN A:191 , LYS A:195 , EDO A:1393 , HOH A:2226 , HOH A:2229 , HOH A:2368BINDING SITE FOR RESIDUE EDO A1403
13BC4SOFTWAREGLN A:97 , HIS A:99 , GLU A:134 , LEU A:249 , HIS A:255 , GLU A:264BINDING SITE FOR RESIDUE EDO A1404
14BC5SOFTWAREASN A:76 , EDO A:1398 , HOH A:2093 , HOH A:2368 , HOH A:2369 , HOH A:2370BINDING SITE FOR RESIDUE EDO A1405
15BC6SOFTWAREALA A:298 , GLY A:299 , GLU A:300 , LEU A:301 , LEU A:302BINDING SITE FOR RESIDUE EDO A1406
16BC7SOFTWAREALA A:40 , PRO A:42 , ARG A:59 , GLU A:80 , LEU A:81 , ASN A:268 , HOH A:2372BINDING SITE FOR RESIDUE EDO A1407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:212 -Pro A:213
2Ser A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WFP)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PMI_I_1PS00965 Phosphomannose isomerase type I signature 1.MANA_SALTY126-134  1A:126-134
2PMI_I_2PS00966 Phosphomannose isomerase type I signature 2.MANA_SALTY255-280  1A:255-280

(-) Exons   (0, 0)

(no "Exon" information available for 2WFP)

(-) 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:389
 aligned with MANA_SALTY | P25081 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:394
                               1                                                                                                                                                                                                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
           MANA_SALTY     - ---MQKLINSVQNYAWGSKTALTELYGIANPQQQPMAELWMGAHPKSSSRITTANGETVSLRDAIEKNKTAMLGEAVANRFGELPFLFKVLCAAQPLSIQVHPNKRNSEIGFAKENAAGIPMDAAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVSLLQPVAGAHSAIAHFLQVPNAERLSQLFASLLNMQGEEKSRALAVLKAALNSQQGEPWQTIRVISEYYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPAGELLTAPVKSGAELDFPIPVDDFAFSLHDLALQETSIGQHSAAILFCVEGEAVLRKDEQRLVLKPGESAFIGADESPVNASGTGRLARVYNKL 391
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------2wfpA02 A:5-149,A:238-275 Jelly Rolls                                                                                                            ----------------------------------------------------------------------------------------2wfpA02 A:5-149,A:238-275 Jelly Rolls -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---PMI_typeI-2wfpA01 A:1-357                                                                                                                                                                                                                                                                                                                                            ---------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.......hhhhhhhh..........eeee........ee.-----.eehhhhhhhhhhhhhhhhhhhhh.....eeeeeee......ee..hhhhhhhhhhhhhhh..................eeeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhheeeeee....eeee.....eeeeeeeeeeee......ee........hhhhhhhh......hhhhh.......................................eeeeeeeeeeeeee..eeeee....eeee.hhhh.eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------PMI_I_1  ------------------------------------------------------------------------------------------------------------------------PMI_I_2  PDB: A:255-280   --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfp A  -2 MASMQKLINSVQNYAWGSKTALTELYGIANPQQQPMAELWMGAHPKSSSRIT-----TVSLRDAIEKNKTAMLGEAVANRFGELPFLFKVLCAAQPLSIQVHPNKRNSEIGFAKENAAGIPMDAAERNYKDPNHKPELVFALTPFLAMNAFREFSDIVSLLQPVAGAHSAIAHFLQVPNAERLSQLFASLLNMQGEEKSRALAVLKAALNSQQGEPWQTIRVISEYYPDDSGLFSPLLLNVVKLNPGEAMFLFAETPHAYLQGVALEVMANSDNVLRAGLTPKYIDIPELVANVKFEPKPAGELLTAPVKSGAELDFPIPVDDFAFSLHDLALQETSIGQHSAAILFCVEGEAVLRKDEQRLVLKPGESAFIGADESPVNASGTGRLARVYNKL 391
                                     7        17        27        37        47 |     |57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387    
                                                                              49    55
   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  (0, 0)

(no "SCOP Domain" information available for 2WFP)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MANA_SALTY | P25081)
molecular function
    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:0004476    mannose-6-phosphate isomerase activity    Catalysis of the reaction: D-mannose 6-phosphate = D-fructose 6-phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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: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.
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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  Cis Peptide Bonds
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  2wfp
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 Related Entries

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        MANA_SALTY | P25081: 3h1m 3h1w 3h1y

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