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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE N-ACETYLMANNOSAMINE-6-P EPIMERASE FROM STREPTOCOCCUS PYOGENES (APC29713) STRUCTURAL GENOMICS, MCSG
 
Authors :  F. J. Rotella, R. G. Zhang, L. E. O. Lezondra, F. R. Collart, A. Joachimia Center For Structural Genomics (Mcsg)
Date :  22 Feb 05  (Deposition) - 05 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Structural Genomics, Epimerase, Streptococcus Pyogenes, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. J. Rotella, R. G. Zhang, L. E. O. Lezondra, F. R. Collart, A. Joachimiak
The 1. 6 A Crystal Structure Of Putative N-Acetylmannosamine-6-P Epimerase From Streptococcus Pyogenes
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 BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NANE
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    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): A (1x)B (1x)
Biological Unit 4 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YXY)

(-) Sites  (0, 0)

(no "Site" information available for 1YXY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:81 -Pro A:82
2Pro B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YXY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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   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:230
 aligned with NANE_STRP1 | P65522 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
           NANE_STRP1     4 KPTKEKLMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQAITDLPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIRQVKEKYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCKAGIAVIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEALK 233
               SCOP domains d1yxya1 A:4-233 Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE                                                                                                                                                              SCOP domains
               CATH domains 1yxyA00 A:4-233 Aldolase class I                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eee...............hhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeee..............hhhhhhhhhh....eeeee..........hhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee................hhhhhhhhhhh...eeee....hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxy A   4 KPTKEKLMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQAITDLPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIRQVKEKYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCKAGIAVIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEALK 233
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with NANE_STRP1 | P65522 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:230
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
           NANE_STRP1     4 KPTKEKLMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQAITDLPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIRQVKEKYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCKAGIAVIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEALK 233
               SCOP domains d1yxyb_ B: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE                                                                                                                                                                   SCOP domains
               CATH domains 1yxyB00 B:4-233 Aldolase class I                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eee...............hhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeee..............hhhhhhhhhh....eeeee..........hhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee................hhhhhhhhhhh...eeee....hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxy B   4 KPTKEKLMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQAITDLPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIRQVKEKYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCKAGIAVIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEALK 233
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YXY)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NANE_STRP1 | P65522)
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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    Pro A:81 - Pro A:82   [ RasMol ]  
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