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(-) Description

Title :  CRYSTAL STRUCTURE OF ANABOLIC ORNITHINE CARBAMOYLTRANSFERASE FROM VIBRIO VULNIFICUS IN COMPLEX WITH CITRULLINE AND INORGANIC PHOSPHATE
 
Authors :  I. G. Shabalin, J. Winsor, S. Grimshaw, M. J. Domagalski, W. F. Anderson Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  20 Mar 13  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase, Carbamoyl Phosphate, L-Ornithine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, J. Winsor, S. Grimshaw, W. Minor
Crystal Structures And Kinetic Properties Of Anabolic Ornithine Carbamoyltransferase From Human Pathogens Vibrio Vulnificus And Bacillus Anthracis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ORNITHINE CARBAMOYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ANABOLIC ORNITHINE CARBAMOYLTRANSFERASE, MONOMER
    Gene: ARGF, VV1_1466
    Organism Scientific: VIBRIO VULNIFICUS CMCP6
    Organism Taxid: 216895
    Strain: CMCP6
    Synonym: OTCASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CIR3Ligand/IonCITRULLINE
2CL3Ligand/IonCHLORIDE ION
3PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
4PO43Ligand/IonPHOSPHATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:57 , THR A:58 , ARG A:59 , THR A:60 , ARG A:108 , CIR A:402 , GLN B:84BINDING SITE FOR RESIDUE PO4 A 401
02AC2SOFTWARETHR A:60 , ARG A:108 , HIS A:135 , GLN A:138 , ASN A:169 , ASP A:233 , SER A:237 , MET A:238 , CYS A:275 , LEU A:276 , ARG A:320 , PO4 A:401 , HOH A:598 , HOH B:619BINDING SITE FOR RESIDUE CIR A 402
03AC3SOFTWARELEU A:13 , PHE A:134 , PRO A:136 , SER A:173 , HOH A:510BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWARELEU A:262 , ASN A:267 , PRO A:268 , HOH A:654BINDING SITE FOR RESIDUE PEG A 404
05AC5SOFTWAREGLY A:295 , HOH A:569BINDING SITE FOR RESIDUE PEG A 405
06AC6SOFTWAREARG A:167 , ALA A:192BINDING SITE FOR RESIDUE PEG A 406
07AC7SOFTWARESER B:57 , THR B:58 , ARG B:59 , THR B:60 , ARG B:108 , CIR B:402 , GLN C:84BINDING SITE FOR RESIDUE PO4 B 401
08AC8SOFTWARETHR B:60 , ARG B:108 , HIS B:135 , GLN B:138 , ASN B:169 , ASP B:233 , SER B:237 , MET B:238 , CYS B:275 , LEU B:276 , ARG B:320 , PO4 B:401 , HOH B:523 , HOH C:515BINDING SITE FOR RESIDUE CIR B 402
09AC9SOFTWARELEU B:13 , PHE B:134 , PRO B:136 , SER B:173 , HOH B:522BINDING SITE FOR RESIDUE CL B 403
10BC1SOFTWARELEU B:262 , ASN B:267 , PRO B:268 , HIS B:310BINDING SITE FOR RESIDUE PEG B 404
11BC2SOFTWAREGLU A:307 , HOH B:622BINDING SITE FOR RESIDUE PEG B 405
12BC3SOFTWAREGLN A:84 , SER C:57 , THR C:58 , ARG C:59 , THR C:60 , ARG C:108 , CIR C:402BINDING SITE FOR RESIDUE PO4 C 401
13BC4SOFTWARETHR C:60 , ARG C:108 , LEU C:130 , HIS C:135 , GLN C:138 , ASN C:169 , ASP C:233 , SER C:237 , MET C:238 , CYS C:275 , LEU C:276 , ARG C:320 , PO4 C:401 , HOH C:520 , HOH C:537BINDING SITE FOR RESIDUE CIR C 402
14BC5SOFTWARELEU C:13 , SER C:173BINDING SITE FOR RESIDUE CL C 403
15BC6SOFTWARELEU C:262 , LYS C:263 , ASN C:267 , HIS C:310BINDING SITE FOR RESIDUE PEG C 404
16BC7SOFTWARELYS C:213 , THR C:215BINDING SITE FOR RESIDUE PEG C 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JQO)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:276 -Pro A:277
2Leu B:276 -Pro B:277
3Leu C:276 -Pro C:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JQO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JQO)

(-) Exons   (0, 0)

(no "Exon" information available for 4JQO)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jqoa1 A:-3-152 automated matches                                                                                                                          d4jqoa2 A:153-334 automated matches                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jqo A  -3 QSNAMAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                     6        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       286       296       306       316       326        


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4jqob1 B:-5-152 automated matches                                                                                                                            d4jqob2 B:153-334 automated matches                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jqo B  -5 YFQSNAMAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4jqoc1 C:1-152 automated matches                                                                                                                       d4jqoc2 C:153-334 automated matches                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jqo C   1 MAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JQO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JQO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OTC_VIBVU | Q8DCF5: 3upd 4h31 4jfr 4jhx 4kwt

(-) Related Entries Specified in the PDB File

4h31 COMPLEX WITH CARBAMOYL PHOSPHATE AND L-NORVALINE
4jfr COMPLEX WITH CARBAMOYL PHOSPHATE
4jhx COMPLEX WITH CARBAMOYL PHOSPHATE AND ARGININE RELATED ID: CSGID-IDP91384 RELATED DB: TARGETTRACK