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(-) Description

Title :  CRYSTAL STRUCTURE OF SIALIC ACID SYNTHASE (NEUB) FROM NEISSERIA MENINGITIDIS IN COMPLEX WITH MG2+ AND (4S)-2-METHYL-2,4-PENTANEDIOL
 
Authors :  A. Rosanally, E. Morrison, P. Berti, M. S. Junop
Date :  27 Nov 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Biosynthetic Protein, Tim Barrel, Antifreeze-Like Domain, Domain-Swapped Dimer, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Morrison, A. Rosanally, M. S. Junop, P. Berti
Crystal Structure Of Sialic Acid Synthase (Neub) From Neisseria Meningitidis In Complex With Mg2+ And (4S)-2-Methyl-2, 4-Pentanediol
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSULE BIOSYNTHESIS PROTEIN
    Chains: A
    EC Number: 4.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PCWORI+
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SYNC, SIAC
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487
    Synonym: SIALIC ACID SYNTHASE, NEUB, SIAC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:25 , HIS A:215 , HIS A:236 , MPD A:4984 , HOH A:5053 , HOH A:5175BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREGLU A:25 , LYS A:53 , GLN A:55 , THR A:110 , PHE A:112 , LYS A:129 , GLY A:131 , TYR A:186 , HIS A:215 , GLU A:234 , MG A:1001 , HOH A:5012 , HOH A:5053 , HOH A:5124BINDING SITE FOR RESIDUE MPD A 4984

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:186 -Pro A:187
2Arg A:314 -Pro A:315

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZDR)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZDR)

(-) 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:348
 aligned with Q57265_NEIME | Q57265 from UniProtKB/TrEMBL  Length:349

    Alignment length:348
                                    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        
         Q57265_NEIME     2 QNNNEFKIGNRSVGYNHEPLIICEIGINHEGSLKTAFEMVDAAYNAGAEVVKHQTHIVEDEMSDEAKQVIPGNADVSIYEIMERCALNEEDEIKLKEYVESKGMIFISTPFSRAAALRLQRMDIPAYKIGSGECNNYPLIKLVASFGKPIILSTGMNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVRLGGMNDLSEAFPDAIIGLSDHTLDNYACLGAVALGGSILERHFTDRMDRPGPDIVCSMNPDTFKELKQGAHALKLARGGKKDTIIAGEKPTKDFAFASVVADKDIKKGELLSGDNLWVKRPGNGDFSVNEYETLFGKVAACNIRKGAQIKKTDIE 349
               SCOP domains d2zdra2 A:2-281 Capsule biosynthesis protein SiaC, N-terminal domain                                                                                                                                                                                                                    d2zdra1 A:282-349                                                    SCOP domains
               CATH domains ----2zdrA01 A:6-276 Aldolase class I                                                                                                                                                                                                                                               ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeehhhhh.hhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhh...eeeee..........hhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.eeee..............eeee.......hhhhhhhhh..............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zdr A   2 QNNNEFKIGNRSVGYNHEPLIICEIGINHEGSLKTAFEMVDAAYNAGAEVVKHQTHIVEDEMSDEAKQVIPGNADVSIYEIMERCALNEEDEIKLKEYVESKGMIFISTPFSRAAALRLQRMDIPAYKIGSGECNNYPLIKLVASFGKPIILSTGMNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVRLGGMNDLSEAFPDAIIGLSDHTLDNYACLGAVALGGSILERHFTDRMDRPGPDIVCSMNPDTFKELKQGAHALKLARGGKKDTIIAGEKPTKDFAFASVVADKDIKKGELLSGDNLWVKRPGNGDFSVNEYETLFGKVAACNIRKGAQIKKTDIE 349
                                    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
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZDR)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q57265_NEIME | Q57265)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016051    carbohydrate biosynthetic process    The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.

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 Related Entries

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

UniProtKB/TrEMBL
        Q57265_NEIME | Q57265: 1xuu 1xuz 3cm4 4ipi 4ipj

(-) Related Entries Specified in the PDB File

1xuu 1xuz