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(-) Description

Title :  CRYSTAL STRUCTURE OF ANABOLIC ORNITHINE CARBAMOYLTRANSFERASE FROM VIBRIO VULNIFICUS IN COMPLEX WITH CARBAMOYLPHOSPHATE AND ARGININE
 
Authors :  I. G. Shabalin, P. Bacal, J. Winsor, S. Grimshaw, M. Grabowski, M. D. Cho L. Shuvalova, W. F. Anderson, W. Minor, Center For Structural Geno Infectious Diseases (Csgid)
Date :  05 Mar 13  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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, Carbamoylphosphate, 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: 469008
    Expression System Vector Type: PLASMID
    Gene: ARGF, VV1_1466
    Organism Scientific: VIBRIO VULNIFICUS
    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, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2CL4Ligand/IonCHLORIDE ION
3CP2Ligand/IonPHOSPHORIC ACID MONO(FORMAMIDE)ESTER
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:57 , THR A:58 , ARG A:59 , THR A:60 , ARG A:108 , HIS A:135 , GLN A:138 , CYS A:275 , LEU A:276 , ARG A:320 , ARG A:403BINDING SITE FOR RESIDUE CP A 401
2AC2SOFTWARELEU A:13 , PHE A:134 , SER A:173 , HOH A:530BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWARELEU A:130 , ASN A:168 , ASN A:169 , ASP A:233 , SER A:237 , MET A:238 , PRO A:277 , CP A:401 , HOH A:519BINDING SITE FOR RESIDUE ARG A 403
4AC4SOFTWARELEU B:13 , PHE B:134 , SER B:173 , HOH B:520BINDING SITE FOR RESIDUE CL B 401
5AC5SOFTWARESER B:57 , ARG B:59 , THR B:60 , HOH B:502BINDING SITE FOR RESIDUE CL B 402
6AC6SOFTWARETRP B:245 , VAL B:290BINDING SITE FOR RESIDUE PEG B 403
7AC7SOFTWARELEU C:13 , PRO C:136 , SER C:173BINDING SITE FOR RESIDUE CL C 401
8AC8SOFTWARESER C:57 , THR C:58 , ARG C:59 , THR C:60 , ARG C:108 , HIS C:135 , GLN C:138 , CYS C:275 , LEU C:276 , ARG C:320 , HOH C:648 , HOH C:653 , HOH C:654BINDING SITE FOR RESIDUE CP C 402

(-) SS Bonds  (0, 0)

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

(-) 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 4JHX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JHX)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jhxa1 A:-1-152 automated matches                                                                                                                        d4jhxa2 A: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
                 4jhx A  -1 NAMAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328      


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4jhxb1 B:3-152 automated matches                                                                                                                     d4jhxb2 B:153-334 automated matches                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee.....hhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhhh......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jhx B   3 FNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   ||  250       260       270       280       290       300       310       320       330    
                                                                                                                                                                                                                                                                   236|                                                                                         
                                                                                                                                                                                                                                                                    245                                                                                         


Chain C from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4jhxc1 C:3-152 automated matches                                                                                                                     d4jhxc2 C:153-334 automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee.....hhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jhx C   3 FNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLGS 334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   ||  249       259       269       279       289       299       309       319       329     
                                                                                                                                                                                                                                                                   236|                                                                                          
                                                                                                                                                                                                                                                                    244
   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 4JHX)

(-) Pfam Domains  (0, 0)

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

(-) 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 4jqo 4kwt

(-) Related Entries Specified in the PDB File

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