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(-) Description

Title :  CRYSTAL STRUCTURE OF B-SUBUNIT OF THE DNA GYRASE FROM MYXOCOCCUS XANTHUS
 
Authors :  U. A. Ramagopal, R. Toro, A. J. Meyer, S. K. Burley, S. C. Almo, New York Research Center For Structural Genomics (Nysgxrc)
Date :  22 Apr 08  (Deposition) - 06 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Unknown Function, Dna Gyrase, B-Subunit, Atp- Binding, Isomerase, Nucleotide-Binding, Topoisomerase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, A. J. Meyer, S. K. Burley, S. C. Almo
Crystal Structure Of B-Subunit Of The Dna Gyrase From Myxococcus Xanthus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA GYRASE, B SUBUNIT, TRUNCATED
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MXAN_5971
    Organism Scientific: MYXOCOCCUS XANTHUS
    Organism Taxid: 246197
    Strain: DK 1622

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CWV)

(-) Sites  (0, 0)

(no "Site" information available for 3CWV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:89 -Pro A:90
2Thr A:139 -Pro A:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CWV)

(-) 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:349
 aligned with Q1CZR7_MYXXD | Q1CZR7 from UniProtKB/TrEMBL  Length:361

    Alignment length:349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347         
         Q1CZR7_MYXXD     8 GGIVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSRTVTAENLVRVATGAGFLGRPPGDGWGWDSMLVVSLALSSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARR 356
               SCOP domains d3cwva1 A:8-206 automated matches                                                                                                                                                                      d3cwva2 A:207-356 automated matches                                                                                                                    SCOP domains
               CATH domains 3cwvA01 A:8-205  [code=3.30.565.10, no name defined]                                                                                                                                                  3cwvA02 A:206-356  [code=3.30.230.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeee...hhhhhhhhhh..hhhhh..........hhhhhhhheeeeeeeeee..eeeeeeee..ee....eee...........eeeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee....eeeeee..hhhhhhhhhhhh.........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeeeee.hhhhh.............hhhhhhhhhhhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cwv A   8 GGIVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSRTVTAENLVRVATGAGFLGRPPGDGWGWDSMLVVSLALSSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARR 356
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347         


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Q1CZR7_MYXXD | Q1CZR7 from UniProtKB/TrEMBL  Length:361

    Alignment length:348
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349        
         Q1CZR7_MYXXD    10 IVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSRTVTAENLVRVATGAGFLGRPPGDGWGWDSMLVVSLALSSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARRT 357
               SCOP domains d3cwvb1 B:10-206 automated matches                                                                                                                                                                   d3cwvb2 B:207-357 automated matches                                                                                                                     SCOP domains
               CATH domains 3cwvB01 B:10-205  [code=3.30.565.10, no name defined]                                                                                                                                               3cwvB02 B:206-357  [code=3.30.230.10, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeee.-----------------------------.hhhhhhhheeeeeeeee-....eeeeee..ee..-------..........eeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee....eeeeee..hhhhhhhhhhhh.........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeeeee.hhhhh.............hhhhhhhhhhhhhhhhhhh...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cwv B  10 IVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTS-----------------------------SMLVVSLALSSRYQVDIW-DGRQWRVMGEHGHPQG-------MEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARRT 357
                                    19        29        39        49        59        69         -         -        99       109      |119       129   |     - |     149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349        
                                                                                      69                            99              116 |            133     141                                                                                                                                                                                                                        
                                                                                                                                      118
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q1CZR7_MYXXD | Q1CZR7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
biological process
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

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  Cis Peptide Bonds
    Arg A:89 - Pro A:90   [ RasMol ]  
    Thr A:139 - Pro A:140   [ RasMol ]  
 
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