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(-) Description

Title :  CRYSTAL STRUCTURE OF AN A PUTATIVE HYDROLASE OF THE ISOCHORISMATASE FAMILY (CV_1320) FROM CHROMOBACTERIUM VIOLACEUM ATCC 12472 AT 1.06 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics, Joint Center For Struct Genomics (Jcsg)
Date :  29 Mar 10  (Deposition) - 23 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isochorismatase Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of An A Putative Hydrolase Of The Isochorismatase Family (Cv_1320) From Chromobacterium Violaceum Atcc 12472 At 1. 06 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CV_1320
    Organism Common: TBD
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 243365
    Strain: ATCC 12472

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric/Biological Unit (3, 23)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2IOD10Ligand/IonIODIDE ION
3MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:45 , ARG A:84 , HOH A:330BINDING SITE FOR RESIDUE IOD A 198
02AC2SOFTWAREHOH A:317BINDING SITE FOR RESIDUE IOD A 199
03AC3SOFTWARETHR A:153 , HOH A:481BINDING SITE FOR RESIDUE IOD A 200
04AC4SOFTWAREPHE A:77 , ARG A:159 , HOH A:343BINDING SITE FOR RESIDUE IOD A 202
05AC5SOFTWAREMSE B:1BINDING SITE FOR RESIDUE IOD A 203
06AC6SOFTWARETRP A:28 , TYR A:68 , SER A:121 , ASN A:124 , PHE A:150 , HOH A:219 , HOH A:252BINDING SITE FOR RESIDUE EDO A 204
07AC7SOFTWAREARG A:58 , ASP A:151 , ARG A:159 , SER A:161 , HOH A:316 , HOH A:322 , HOH A:348 , HOH A:370 , HOH A:462BINDING SITE FOR RESIDUE EDO A 205
08AC8SOFTWAREARG A:50 , HOH A:413 , HOH A:415BINDING SITE FOR RESIDUE EDO A 206
09AC9SOFTWAREPRO A:53 , LEU A:54 , ILE A:55 , THR A:88 , TRP A:112 , MSE B:1BINDING SITE FOR RESIDUE EDO A 207
10BC1SOFTWAREGLN B:45 , ARG B:84BINDING SITE FOR RESIDUE IOD B 200
11BC2SOFTWAREGLY B:86 , THR B:153BINDING SITE FOR RESIDUE IOD B 201
12BC3SOFTWAREPRO B:53 , LEU B:54 , ILE B:55 , THR B:88 , TRP B:112 , HOH B:419BINDING SITE FOR RESIDUE EDO B 202
13BC4SOFTWARESER B:8 , GLY B:111 , LEU B:113 , GLU B:114 , HOH B:408 , HOH B:423BINDING SITE FOR RESIDUE EDO B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:120 -Ser A:121
2Val B:120 -Ser B:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MCW)

(-) 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:195
 aligned with Q7NYF4_CHRVO | Q7NYF4 from UniProtKB/TrEMBL  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
         Q7NYF4_CHRVO     3 APLRFSSDKPLLLLIDMQQAVDDPSWGPRNHPQAEQACAGLLQAWRARGLPLIHIRHDSVEPNSTYRPGQPGHAFKPEVEPRPGETVIAKQTNSAFIGTGLEALLRANGWLELVVAGVSTSNSVEATVRMAGNLGFAVCLAEDGCFTFDKTDWHGRRRSADEVHAMSLANLDGEYCRVCGSADILAALGNIAGAA 197
               SCOP domains d3mcwa_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeee............hhhhh.hhhhh.....eeeee.........hhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee...ee.....eehhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcw A   3 APLRFSSDKPLLLLIDmQQAVDDPSWGPRNHPQAEQACAGLLQAWRARGLPLIHIRHDSVEPNSTYRPGQPGHAFKPEVEPRPGETVIAKQTNSAFIGTGLEALLRANGWLELVVAGVSTSNSVEATVRmAGNLGFAVCLAEDGCFTFDKTDWHGRRRSADEVHAmSLANLDGEYCRVCGSADILAALGNIAGAA 197
                                    12      | 22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     | 172       182       192     
                                           19-MSE                                                                                                          132-MSE                             168-MSE                         


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with Q7NYF4_CHRVO | Q7NYF4 from UniProtKB/TrEMBL  Length:197

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
         Q7NYF4_CHRVO     1 MPAPLRFSSDKPLLLLIDMQQAVDDPSWGPRNHPQAEQACAGLLQAWRARGLPLIHIRHDSVEPNSTYRPGQPGHAFKPEVEPRPGETVIAKQTNSAFIGTGLEALLRANGWLELVVAGVSTSNSVEATVRMAGNLGFAVCLAEDGCFTFDKTDWHGRRRSADEVHAMSLANLDGEYCRVCGSADILAALGNI 193
               SCOP domains d3mcwb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Isochorismatase-3mcwB01 B:12-185                                                                                                                                              -------- Pfam domains (1)
           Pfam domains (2) -----------Isochorismatase-3mcwB02 B:12-185                                                                                                                                              -------- Pfam domains (2)
         Sec.struct. author ............eeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeee............hhhhh.hhhhh.....eeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh.eeeeeeeeee...ee.....eehhhhhhhhhhhhhh....eeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcw B   1 mPAPLRFSSDKPLLLLIDmQQAVDDPSWGPRNHPQAEQACAGLLQAWRARGLPLIHIRHDSVEPNSTYRPGQPGHAFKPEVEPRPGETVIAKQTNSAFIGTGLEALLRANGWLELVVAGVSTSNSVEATVRmAGNLGFAVCLAEDGCFTFDKTDWHGRRRSADEVHAmSLANLDGEYCRVCGSADILAALGNI 193
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130 |     140       150       160       170       180       190   
                            1-MSE            19-MSE                                                                                                          132-MSE                             168-MSE
   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  (0, 0)

(no "CATH Domain" information available for 3MCW)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Isochorismatase] (9)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7NYF4_CHRVO | Q7NYF4)
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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    Val A:120 - Ser A:121   [ RasMol ]  
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