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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI DIAA
 
Authors :  K. Keyamura, N. Fujikawa, T. Ishida, S. Ozaki, M. Suetsugu, W. Kagawa, S. Yokoyama, H. Kurumizaka, T. Katayama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Apr 07  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Intermolecular Disulfide Bonding, Putative Phosphosugar Binding Protein, Dnaa Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Keyamura, N. Fujikawa, T. Ishida, S. Ozaki, M. Suetsugu, K. Fujimitsu, W. Kagawa, S. Yokoyama, H. Kurumizaka, T. Katayama
The Interaction Of Diaa And Dnaa Regulates The Replication Cycle In E. Coli By Directly Promoting Atp Dnaa-Specific Initiation Complexes
Genes Dev. V. 21 2083 2007
PubMed-ID: 17699754  |  Reference-DOI: 10.1101/GAD.1561207

(-) Compounds

Molecule 1 - DNAA INITIATOR-ASSOCIATING PROTEIN DIAA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DIAA(YRAO)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PUTATIVE PHOSPHOHEPTOSE ISOMERASE, DIAA (YRAO)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2YVA)

(-) Sites  (0, 0)

(no "Site" information available for 2YVA)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:8 -B:181
2A:181 -B:8

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.DIAA_ECOLI34-196
 		  2A:34-193
B:34-193
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.DIAA_ECOLI34-196
 		  4A:34-193
B:34-193

(-) Exons   (0, 0)

(no "Exon" information available for 2YVA)

(-) 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:193
 aligned with DIAA_ECOLI | P66817 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
           DIAA_ECOLI     1 MQERIKACFTESIQTQIAAAEALPDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLTAIANDRLHDEVYAKQVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEIRIPSHRSARIQEMHMLTVNCLCDLIDNTLFPH 193
               SCOP domains d2yvaa_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2yvaA00 A:1-193 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..........eee...hhhhhhhhh...hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeee...hhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SIS  PDB: A:34-193 UniProt: 34-196                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yva A   1 MQERIKACFTESIQTQIAAAEALPDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLTAIANDRLHDEVYAKQVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEIRIPSHRSARIQEMHMLTVNCLCDLIDNTLFPH 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with DIAA_ECOLI | P66817 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
           DIAA_ECOLI     1 MQERIKACFTESIQTQIAAAEALPDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLTAIANDRLHDEVYAKQVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEIRIPSHRSARIQEMHMLTVNCLCDLIDNTLFPH 193
               SCOP domains d2yvab_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains 2yvaB00 B:1-193 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                              CATH domains
           Pfam domains (1) -------SIS_2-2yvaB01 B:8-144                                                                                                                    ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------SIS_2-2yvaB02 B:8-144                                                                                                                    ------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..........eee...hhhhhhhhh...hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeee...hhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------SIS  PDB: B:34-193 UniProt: 34-196                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yva B   1 MQERIKACFTESIQTQIAAAEALPDAISRAAMTLVQSLLNGNKILCCGNGTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLTAIANDRLHDEVYAKQVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYDGGELAGLLGPQDVEIRIPSHRSARIQEMHMLTVNCLCDLIDNTLFPH 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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: SIS (53)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DIAA_ECOLI | P66817)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0032298    positive regulation of DNA-dependent DNA replication initiation    Any process that activates or increases the frequency, rate or extent of initiation of DNA-dependent DNA replication.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DIAA_ECOLI | P66817: 4u6n

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