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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A PUTATIVE NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  A. J. Stein, M. E. Cuff, A. Sather, G. Shackelford, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date :  08 Apr 09  (Deposition) - 21 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleotidylyl, Transferase, Mcsg, Midwest Center For Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, M. E. Cuff, A. Sather, G. Shackelford, A. Joachimiak
The Crystal Structure Of A Putative Nicotinate-Nucleotide Adenylyltransferase From Vibrio Parahaemolyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN VPA0413
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670
    Strain: RIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:11 , ASN A:12 , HIS A:18 , HOH A:185BINDING SITE FOR RESIDUE CL A 178
2AC2SOFTWAREPHE B:11 , ASN B:12 , HIS B:18 , SER B:139 , HOH B:242BINDING SITE FOR RESIDUE CL B 178

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H05)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:12 -Pro A:13
2Asn B:12 -Pro B:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H05)

(-) Exons   (0, 0)

(no "Exon" information available for 3H05)

(-) 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:155
 aligned with Q87J40_VIBPA | Q87J40 from UniProtKB/TrEMBL  Length:177

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
         Q87J40_VIBPA     1 MKKIAIFGSAFNPPSLGHKSVIESLSHFDLVLLEPSIAHAWGKNMLDYPIRCKLVDAFIKDMGLSNVQRSDLEQALYQPGQSVTTYALLEKIQEIYPTADITFVIGPDNFFKFAKFYKAEEITERWTVMACPEKVKIRSTDIRNALIEGKDISTYTTPTVSELLLN 166
               SCOP domains d3h05a_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 3h05A00 A:1-166 Tyrosyl-Transfer RNA        Synthetase , subunit E, domain 1                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhh......eeeeee..-------..hhhhhhhhhhhhhhhhh...eee.hhhhhhh----..hhhhhhhhhhhhh...eeeeeehhhhhhhhhhh.hhhhhhhhheeee.......hhhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h05 A   1 MKKIAIFGSAFNPPSLGHKSVIESLSHFDLVLLEPSI-------MLDYPIRCKLVDAFIKDMGLSNVQRSDLEQALY----SVTTYALLEKIQEIYPTADITFVIGPDNFFKFAKFYKAEEITERWTVMACPEKVKIRSTDIRNALIEGKDISTYTTPTVSELLLN 166
                                    10        20        30      |  -    |   50        60        70      |  - |      90       100       110       120       130       140       150       160      
                                                               37      45                              77   82                                                                                    


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with Q87J40_VIBPA | Q87J40 from UniProtKB/TrEMBL  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         Q87J40_VIBPA     1 MKKIAIFGSAFNPPSLGHKSVIESLSHFDLVLLEPSIAHAWGKNMLDYPIRCKLVDAFIKDMGLSNVQRSDLEQALYQPGQSVTTYALLEKIQEIYPTADITFVIGPDNFFKFAKFYKAEEITERWTVMACPEKVKIRSTDIRNALIEGKDISTYTTPTVSELLLNEGLYRETLSGK 177
               SCOP domains d3h05b_ B: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhh......eeeeee..------...hhhhhhhhhhhhhhhhh...eee.hhhhhhh-----.hhhhhhhhhhhhh...eeeeeehhhhhhhhhhh.hhhhhhhhheeee.....---hhhhhhhhhhh.......hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h05 B   1 MKKIAIFGSAFNPPSLGHKSVIESLSHFDLVLLEPSI------NMLDYPIRCKLVDAFIKDMGLSNVQRSDLEQALY-----VTTYALLEKIQEIYPTADITFVIGPDNFFKFAKFYKAEEITERWTVMACPEKV---STDIRNALIEGKDISTYTTPTVSELLLNEGLYRETLSGK 177
                                    10        20        30      |  -   |    50        60        70      |  -  |     90       100       110       120       130    |  140       150       160       170       
                                                               37     44                               77    83                                                 135 139
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H05)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87J40_VIBPA | Q87J40)
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.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  3h05
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