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(-) Description

Title :  CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM ACTINOBACILLUS SUCCINOGENES
 
Authors :  V. N. Malashkevich, R. Toro, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  28 Jan 08  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Isomerase, Transcription, Transcription Regulation, Psi-2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of An Uncharacterized Protein From Actinobacillus Succinogenes.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALANINE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 54-327
    Gene: ASUC_0357
    Organism Scientific: ACTINOBACILLUS SUCCINOGENES
    Organism Taxid: 339671
    Strain: 130Z

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:21 , ASP B:223 , ILE B:224BINDING SITE FOR RESIDUE CL B 301
2AC2SOFTWAREASN A:20 , PHE A:22 , TYR A:138 , ARG A:142 , ASP A:220 , GLN A:237 , HOH A:325BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREASN B:20 , PHE B:22 , TYR B:138 , ARG B:142 , ASP B:220 , GLN B:237 , HOH B:320 , HOH B:400BINDING SITE FOR RESIDUE GOL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C3K)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ile A:210 -Pro A:211
2Val A:229 -Pro A:230
3Ser A:256 -Asp A:257
4Ile B:210 -Pro B:211
5Val B:229 -Pro B:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C3K)

(-) Exons   (0, 0)

(no "Exon" information available for 3C3K)

(-) 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:267
 aligned with A6VL88_ACTSZ | A6VL88 from UniProtKB/TrEMBL  Length:327

    Alignment length:272
                                                                                                                                                                                                                                                                                                        327 
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326| 
         A6VL88_ACTSZ    57 KTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCNTESDLARSRSCLTLLSGKMVDGVITMDALSELPELQNIIGAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYSRISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVGFDGVDISQITVPALTTVQQPSEQIGMKAVSLLLEQIHSDVLAKTVHHLLPWKFVRRQSS-   -
               SCOP domains d3c3ka_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3c3kA01 A:7-107,A:237-269  [code=3.40.50.2300, no name defined]                                      3c3kA02 A:108-236,A:270-278  [code=3.40.50.2300, no name defined]                                                                3c3kA01 A:7-107,A:237     -269   3c3kA02   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh...eeee..........eee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhhhhh..-----.eee...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3k A   7 KTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCNTESDLARSRSCLTLLSGKMVDGVITMDALSELPELQNIIGAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYSRISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVGFDGVDISQITVPALTTVQQPSEQIGMKAVSLLLEQIHSD-----VHHLLPWKFVRRQSSE 278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256|     |266       276  
                                                                                                                                                                                                                                                                                    257   263               


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with A6VL88_ACTSZ | A6VL88 from UniProtKB/TrEMBL  Length:327

    Alignment length:272
                                                                                                                                                                                                                                                                                                        327 
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326| 
         A6VL88_ACTSZ    57 KTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCNTESDLARSRSCLTLLSGKMVDGVITMDALSELPELQNIIGAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYSRISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVGFDGVDISQITVPALTTVQQPSEQIGMKAVSLLLEQIHSDVLAKTVHHLLPWKFVRRQSS-   -
               SCOP domains d3c3kb_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3c3kB01 B:7-107,B:237-269  [code=3.40.50.2300, no name defined]                                      3c3kB02 B:108-236,B:270-278  [code=3.40.50.2300, no name defined]                                                                3c3kB01 B:7-107,B:237-269        3c3kB02   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhh...eeee.........eeee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eee....hhhhhh......eee.hhhhhhhhhhhhhhhhhh........eee...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3k B   7 KTGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCNTESDLARSRSCLTLLSGKMVDGVITMDALSELPELQNIIGAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHGLDYSRISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVGFDGVDISQITVPALTTVQQPSEQIGMKAVSLLLEQIHSDVLAKTVHHLLPWKFVRRQSSE 278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C3K)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6VL88_ACTSZ | A6VL88)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008784    alanine racemase activity    Catalysis of the reaction: L-alanine = D-alanine.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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