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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE MANNAC-6-P EPIMERASE FROM STAPHYLOCOCCUS AUREUS (STRAIN N315)
 
Authors :  C. Chang, A. Joachimiak, H. Li, Midwest Center For Structural Geno (Mcsg)
Date :  15 Nov 04  (Deposition) - 28 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Mannac-6-P Epimerase, Nane, Structural Genomics, Protein Structure Initiative, Psi, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, S. Moy, H. Li, A. Joachimiak
Crystal Structure Of Putative Mannac-6-P Epimerase From Staphylococcus Aureus (Strain N315)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMSCG7
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NANE
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: N315
    Synonym: MANNAC-6-P EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 17)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:9 , ARG A:208 , PO4 A:502 , HOH A:515 , HOH A:556 , HOH A:572 , HOH A:584 , HOH A:613BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWAREASN A:182 , GLY A:203 , GLY A:204 , PO4 A:501 , HOH A:516 , HOH A:550 , HOH A:556 , HOH A:572 , HOH A:589 , HOH A:627BINDING SITE FOR RESIDUE PO4 A 502
3AC3SOFTWAREGLY B:181 , ASN B:182 , GLY B:203 , GLY B:204 , HOH B:518 , HOH B:547 , HOH B:566 , HOH B:605 , HOH B:615 , HOH B:665BINDING SITE FOR RESIDUE PO4 B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y0E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y0E)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y0E)

(-) Sequences/Alignments

Asymmetric 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:222
 aligned with NANE_STAAN | P65517 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:222
                             1                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
           NANE_STAAN     - -MLPHGLIVSCQALADEPLHSSFIMSKMALAAYEGGAVGIRANTKEDILAIKETVDLPVIGIVKRDYDHSDVFITATSKEVDELIESQCEVIALDATLQQRPKETLDELVSYIRTHAPNVEIMADIATVEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDMYKRVMDLGVHCSVVGGAITRPKEITKRFVQVME 221
               SCOP domains d1y0ea_ A: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE                                                                                                                                                           SCOP domains
               CATH domains 1y0eA00 A:0-221 Aldolase class I                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh...eeee..............hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee...............hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y0e A   0 AmLPHGLIVSCQALPDEPLHSSFImSKmALAAYEGGAVGIRANTKEDILAIKETVDLPVIGIVKRDYDHSDVFITATSKEVDELIESQCEVIALDATLQQRPKETLDELVSYIRTHAPNVEImADIATVEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDmYKRVmDLGVHCSVVGGAITRPKEITKRFVQVmE 221
                             |       9        19    |  |29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189   |   199       209       219| 
                             |                     24-MSE                                                                                           122-MSE                                                           188-MSE|                        220-MSE
                             1-MSE                    27-MSE                                                                                                                                                               193-MSE                        


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with NANE_STAAN | P65517 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:222
                             1                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219  
           NANE_STAAN     - -MLPHGLIVSCQALADEPLHSSFIMSKMALAAYEGGAVGIRANTKEDILAIKETVDLPVIGIVKRDYDHSDVFITATSKEVDELIESQCEVIALDATLQQRPKETLDELVSYIRTHAPNVEIMADIATVEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDMYKRVMDLGVHCSVVGGAITRPKEITKRFVQVME 221
               SCOP domains d1y0eb_ B: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE                                                                                                                                                           SCOP domains
               CATH domains 1y0eB00 B:0-221 Aldolase class I                                                                                                                                                                                               CATH domains
           Pfam domains (1) ------------------------NanE-1y0eB01 B:24-221                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) ------------------------NanE-1y0eB02 B:24-221                                                                                                                                                                                  Pfam domains (2)
         Sec.struct. author ......eeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeee..............hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee...............hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y0e B   0 AmLPHGLIVSCQALPDEPLHSSFImSKmALAAYEGGAVGIRANTKEDILAIKETVDLPVIGIVKRDYDHSDVFITATSKEVDELIESQCEVIALDATLQQRPKETLDELVSYIRTHAPNVEImADIATVEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDmYKRVmDLGVHCSVVGGAITRPKEITKRFVQVmE 221
                             |       9        19    |  |29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189   |   199       209       219| 
                             |                     24-MSE                                                                                           122-MSE                                                           188-MSE|                        220-MSE
                             1-MSE                    27-MSE                                                                                                                                                               193-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NANE_STAAN | P65517)
molecular function
    GO:0047465    N-acylglucosamine-6-phosphate 2-epimerase activity    Catalysis of the reaction: N-acyl-D-glucosamine 6-phosphate = N-acyl-D-mannosamine 6-phosphate.
    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:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
    GO:0006051    N-acetylmannosamine metabolic process    The chemical reactions and pathways involving N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose.
    GO:0019262    N-acetylneuraminate catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    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: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.

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