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(-) Description

Title :  THE STRUCTURE OF PUTATIVE DIHYDROOROTASE FROM PORPHYROMONAS GINGIVALIS.
 
Authors :  M. E. Cuff, M. Borovilos, S. Moy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  04 May 06  (Deposition) - 06 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Porphyromonas Gingivalis, Dihydroorotase, Zinc-Binding Protein, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, M. Borovilos, S. Moy, A. Joachimiak
The Structure Of Putative Dihydroorotase From Porphyromonas Gingivalis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROOROTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PYRC
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 22)

Asymmetric/Biological Unit (8, 22)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CAC2Ligand/IonCACODYLATE ION
3CL1Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
6MSE7Mod. Amino AcidSELENOMETHIONINE
7SO45Ligand/IonSULFATE ION
8ZN2Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:63 , KCX A:149 , HIS A:181 , HIS A:239 , ZN A:602 , CAC A:603 , HOH A:976BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWAREGLN A:63 , HIS A:65 , KCX A:149 , ASP A:313 , ZN A:601 , HOH A:976BINDING SITE FOR RESIDUE ZN A 602
03AC3SOFTWAREHIS A:65 , ASN A:97 , KCX A:149 , PHE A:151 , SER A:154 , SER A:155 , HIS A:181 , ZN A:601 , HOH A:820 , HOH A:857BINDING SITE FOR RESIDUE CAC A 603
04AC4SOFTWAREARG A:6 , ALA A:38 , HOH A:866BINDING SITE FOR RESIDUE CAC A 604
05AC5SOFTWAREPRO A:334 , LEU A:335 , HIS A:338 , SER A:408 , HOH A:635BINDING SITE FOR RESIDUE CL A 605
06AC6SOFTWAREARG A:439 , HOH A:800 , HOH A:910 , HOH A:955 , HOH A:1085BINDING SITE FOR RESIDUE SO4 A 606
07AC7SOFTWARELYS A:198 , VAL A:442 , HIS A:443 , PRO A:444 , HOH A:663 , HOH A:724 , HOH A:995BINDING SITE FOR RESIDUE SO4 A 607
08AC8SOFTWARESER A:-2 , THR A:441 , HOH A:641 , HOH A:1090BINDING SITE FOR RESIDUE SO4 A 608
09AC9SOFTWARETYR A:218 , ARG A:219 , HOH A:911 , HOH A:980BINDING SITE FOR RESIDUE SO4 A 609
10BC1SOFTWAREARG A:295 , GOL A:614 , HOH A:1017 , HOH A:1025BINDING SITE FOR RESIDUE SO4 A 610
11BC2SOFTWARESER A:-2 , ASN A:-1 , CYS A:427 , ARG A:439 , HOH A:677BINDING SITE FOR RESIDUE BME A 611
12BC3SOFTWAREILE A:134 , ILE A:137 , LYS A:138 , GLU A:173 , CYS A:174 , HOH A:1100BINDING SITE FOR RESIDUE BME A 612
13BC4SOFTWAREGLU A:168 , GLY A:172 , GLU A:173 , LEU A:318 , LEU A:319 , CYS A:405 , HOH A:1071 , HOH A:1093BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWARETRP A:270 , ARG A:295 , ARG A:299 , GLN A:349 , SO4 A:610 , HOH A:936 , HOH A:1017 , HOH A:1025 , HOH A:1092 , HOH A:1094BINDING SITE FOR RESIDUE GOL A 614

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:68 -Pro A:69
2Asn A:99 -Pro A:100
3Asn A:286 -Pro A:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GWN)

(-) 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:451
 aligned with Q7MVW1_PORGI | Q7MVW1 from UniProtKB/TrEMBL  Length:449

    Alignment length:451
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                               |     7        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       357       367       377       387       397       407       417       427       437       447 
         Q7MVW1_PORGI     - ---MKILLRNALITNEGKTFPGSVMIDGAFISRIIEGELPADDNLSADEVIECSGLRLFPGCIDDQVHFREPGLTHKATIASESRAAVAGGVTSFMDMPNTNPPTTMWERLLEKRQIGADTAWANYGFFFGGTNDNIDEIKRVDKHLVPGLKLFLGSSTGNMLVDNKETLEKIFGECDLLIATHCEKEEIIRANKEHYKAKYGNDLDIHFHPLIRSEEACYRSSAEAVELAERMNARLHILHLSTEKELSLFRNDIPTAQKRITSEVCVHHLWFSDTDYGRLGNRIKWNPAIKKESDREALRAAVRNGRIDIIATDHAPHLLREKEGSCLQAASGGPLVQHSLLALLELCNQGIFSIEEIVSKTAHIPATLFAIEKRGYIRPGYYADLVLVDPSSPHTVSADNILSLCGWSPFEGFTFSHSVAYTFVNGCLAYAKGRLAESRPTVHPLFFN 448
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gwnA01 A:-2-58,A:377-391,A:416-437                          2gwnA02 A:59-370,A:392-415 Metal-dependent hydrolases                                                                                                                                                                                                                                                                   ------2gwnA01        2gwnA02                 2gwnA01               ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee..eeeeeeeeee..eeeeeee............eeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee.ee....hhhhhhh........eeee....hhhhh..hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhh....hhhhh.eeeeeehhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eee......hhhhhh..............hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..............eeeee....ee..................ee..eeeeeee..eeeee..ee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gwn A  -2 SNAmKILLRNALITNEGKTFPGSVmIDGAFISRIIEGELPADDNLSADEVIECSGLRLFPGCIDDQVHFREPGLTHKATIASESRAAVAGGVTSFmDmPNTNPPTTmWERLLEKRQIGADTAWANYGFFFGGTNDNIDEIKRVDKHLVPGLkLFLGSSTGNmLVDNKETLEKIFGECDLLIATHCEKEEIIRANKEHYKAKYGNDLDIHFHPLIRSEEACYRSSAEAVELAERmNARLHILHLSTEKELSLFRNDIPTAQKRITSEVCVHHLWFSDTDYGRLGNRIKWNPAIKKESDREALRAAVRNGRIDIIATDHAPHLLREKEGSCLQAASGGPLVQHSLLALLELCNQGIFSIEEIVSKTAHIPATLFAIEKRGYIRPGYYADLVLVDPSSPHTVSADNILSLCGWSPFEGFTFSHSVAYTFVNGCLAYAKGRLAESRPTVHPLFFN 448
                               |     7        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       357       367       377       387       397       407       417       427       437       447 
                               |                   22-MSE                                                                 93-MSE    104-MSE                                      149-KCX   159-MSE                                                                 231-MSE                                                                                                                                                                                                                     
                               1-MSE                                                                                        95-MSE
   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  (0, 0)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GWN)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7MVW1_PORGI | Q7MVW1)
molecular function
    GO:0004151    dihydroorotase activity    Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
    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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0016812    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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