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(-) Description

Title :  CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YCKF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YCKF, BSU03450
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1VIV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.PHI_BACSU29-172
 		  2A:29-172
B:29-172
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.PHI_BACSU29-172
 		  2A:29-172
B:29-172
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.PHI_BACSU29-172
 		  4A:29-172
B:29-172

(-) Exons   (0, 0)

(no "Exon" information available for 1VIV)

(-) 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:184
 aligned with PHI_BACSU | P42404 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
            PHI_BACSU     1 MKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETMFTHHANL 184
               SCOP domains d1viva_ A: Hypothetical protein YckF                                                                                                                                                     SCOP domains
               CATH domains 1vivA00 A:1-184 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SIS  PDB: A:29-172 UniProt: 29-172                                                                                                              ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viv A   1 LKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETMFTHHANL 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PHI_BACSU | P42404 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
            PHI_BACSU     1 MKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETM 177
               SCOP domains d1vivb_ B: Hypothetical protein YckF                                                                                                                                              SCOP domains
               CATH domains 1vivB00 B:1-177 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                              CATH domains
           Pfam domains (1) -------------------------------SIS-1vivB01 B:32-157                                                                                                          -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------SIS-1vivB02 B:32-157                                                                                                          -------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.............eeeee.....hhhhhhhhhhhhh...eeeeee....hhhhhhh.eeee...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SIS  PDB: B:29-172 UniProt: 29-172                                                                                                              ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viv B   1 LKTTEYVAEILNELHNSAAYISNEEADQLADHILSSHQIFTAGAGRSGLMAKSFAMRLMHMGFNAHIVGEILTPPLAEGDLVIIGSGSGETKSLIHTAAKAKSLHGIVAALTINPESSIGKQADLIIRMPGSPKDQSNGSYKTIQPMGSLFEQTLLLFYDAVILKLMEKKGLDSETM 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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)
(-)
Family: SIS (23)
(-)
Bacillus subtilis (2)
1aSIS-1vivB01B:32-157
1bSIS-1vivB02B:32-157

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHI_BACSU | P42404)
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:0004360    glutamine-fructose-6-phosphate transaminase (isomerizing) activity    Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate.
    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.
biological process
    GO:0006047    UDP-N-acetylglucosamine metabolic process    The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    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:0019647    formaldehyde assimilation via ribulose monophosphate cycle    The pathway in which formaldehyde is used as a carbon source in the ribulose monophosphate cycle. Methanotrophic bacteria produce formaldehyde from the oxidation of methane and methanol, and then assimilate it via the ribulose monophosphate cycle to form intermediates of the central metabolic routes that are subsequently used for biosynthesis of cell material. Three molecules of formaldehyde are assimilated, forming a three-carbon intermediate of central metabolism; in this pathway, all cellular carbon is assimilated at the oxidation level of formaldehyde.
    GO:0006002    fructose 6-phosphate metabolic process    The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

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  1viv
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 Related Entries

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

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        PHI_BACSU | P42404: 1m3s

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