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(-) Description

Title :  CRYSTAL STRUCTURE OF HALOACID DELAHOGENASE-LIKE FAMILY HYDROLASE (NP_639141.1) FROM XANTHOMONAS CAMPESTRIS AT 1.81 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Apr 07  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_639141. 1, Haloacid Delahogenase-Like Family Hydrolase, 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 Haloacid Delahogenase-Like Family Hydrolase (Np_639141. 1) From Xanthomonas Campestris At 1. 81 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HALOACID DELAHOGENASE-LIKE FAMILY HYDROLASE
    Atcc: 33913
    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: NP_639141.1, XCC3796
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: NCPPB 528, LMG 568

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG2Ligand/IonMAGNESIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:18 , ASP A:20 , ASN A:186 , HOH A:302 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWAREASP B:18 , ASP B:20 , ASN B:186 , HOH B:304 , HOH B:305 , HOH B:306BINDING SITE FOR RESIDUE MG B 300
3AC3SOFTWAREASP A:136 , GLN A:140 , HOH A:365BINDING SITE FOR RESIDUE CL A 301
4AC4SOFTWAREGLY B:135 , ASP B:136 , GLN B:140 , HOH B:336 , HOH B:342BINDING SITE FOR RESIDUE CL B 301
5AC5SOFTWARELYS A:72 , GLY B:70 , GLY B:73BINDING SITE FOR RESIDUE CL B 302
6AC6SOFTWARETYR B:29 , ASP B:36 , HIS B:108BINDING SITE FOR RESIDUE PEG B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PKE)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Mse A:52 -Gln A:53
2Mse B:52 -Gln B:53
3Gln B:54 -His B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PKE)

(-) Exons   (0, 0)

(no "Exon" information available for 2PKE)

(-) 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:233
 aligned with Q8P4B4_XANCP | Q8P4B4 from UniProtKB/TrEMBL  Length:250

    Alignment length:251
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
         Q8P4B4_XANCP     - -MTPIAQRDGQAIQLVGFDGDDTLWKSEDYYRTAEADFEAILSGYLDLGDSRMQQHLLAVERRNLKIFGYGAKGMTLSMIETAIELTEARIEARDIQRIVEIGRATLQHPVEVIAGVREAVAAIAADYAVVLITKGDLFHQEQKIEQSGLSDLFPRIEVVSEKDPQTYARVLSEFDLPAERFVMIGNSLRSDVEPVLAIGGWGIYTPYAVTWAHEQDHGVAADEPRLREVPDPSGWPAAVRALDAQAGRQQ 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pkeA01 A:0-26,A:110-249   2pkeA02 A:27-109 Put     ative phosphatase; domain 2                               2pkeA01 A:0-26,A:110-249  [code=3.40.50.1000, no name defined]                                                                              - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee........hhhhhhhhhhhhhhhhh....-----...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.hhh.eeeee......hhhhhhh..eeee....-------------....eee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pke A   0 GmTPIAQRDGQAIQLVGFDGDDTLWKSEDYYRTAEADFEAILSGYLD-----mQQHLLAVERRNLKIFGYGAKGmTLSmIETAIELTEARIEARDIQRIVEIGRATLQHPVEVIAGVREAVAAIAADYAVVLITKGDLFHQEQKIEQSGLSDLFPRIEVVSEKDPQTYARVLSEFDLPAERFVmIGNSLRSDVEPVLAIGGWGIYTPYA-------------DEPRLREVPDPSGWPAAVRALDAQAGRQQ 250
                             |       9        19        29        39      |  -  |     59        69    |   79        89        99       109       119       129       139       149       159       169       179   |   189       199        |-         -  |    229       239       249 
                             |                                           46     |                    74-MSE                                                                                                      183-MSE                  208           222                            
                             1-MSE                                             52-MSE                    78-MSE                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with Q8P4B4_XANCP | Q8P4B4 from UniProtKB/TrEMBL  Length:250

    Alignment length:241
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 
         Q8P4B4_XANCP     9 GQAIQLVGFDGDDTLWKSEDYYRTAEADFEAILSGYLDLGDSRMQQHLLAVERRNLKIFGYGAKGMTLSMIETAIELTEARIEARDIQRIVEIGRATLQHPVEVIAGVREAVAAIAADYAVVLITKGDLFHQEQKIEQSGLSDLFPRIEVVSEKDPQTYARVLSEFDLPAERFVMIGNSLRSDVEPVLAIGGWGIYTPYAVTWAHEQDHGVAADEPRLREVPDPSGWPAAVRALDAQAGRQ 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pkeB01           2pkeB02 B:27-109 Putative phosphat      ase; domain 2                              2pkeB01 B:9-26,B:110-249  [code=3.40.50.1000, no name defined]                                                                               CATH domains
           Pfam domains (1) ------HAD_2-2pkeB01 B:15-205                                                                                                                                                                         --       ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------HAD_2-2pkeB02 B:15-205                                                                                                                                                                         --       ----------------------------------- Pfam domains (2)
         Sec.struct. author .....eeee........hhhhhhhhhhhhhhhhh..................------...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh..hhh.eeeee......hhhhhhh..eeee...-------...........eee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pke B   9 GQAIQLVGFDGDDTLWKSEDYYRTAEADFEAILSGYLDLGDSRmQQHLLAVE------FGYGAKGmTLSmIETAIELTEARIEARDIQRIVEIGRATLQHPVEVIAGVREAVAAIAADYAVVLITKGDLFHQEQKIEQSGLSDLFPRIEVVSEKDPQTYARVLSEFDLPAERFVmIGNSLRSDVEPVLAIGGWGIYTPY-------QDHGVAADEPRLREVPDPSGWPAAVRALDAQAGRQ 249
                                    18        28        38        48   |    58 |      68     |  78        88        98       108       118       128       138       148       158       168       178    |  188       198        |-      |218       228       238       248 
                                                                      52-MSE  60     67     74-MSE                                                                                                      183-MSE                 207     215                                  
                                                                                                78-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  (0, 0)

(no "SCOP Domain" information available for 2PKE)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8P4B4_XANCP | Q8P4B4)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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