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(-) Description

Title :  CRYSTAL STRUCTURE OF ANABOLIC ORNITHINE CARBAMOYLTRANSFERASE FROM VIBRIO VULNIFICUS IN COMPLEX WITH CARBAMOYL PHOSPHATE AND L-NORVALINE
 
Authors :  I. G. Shabalin, J. Winsor, S. Grimshaw, T. Osinski, M. D. Chordia, L. Shu W. F. Anderson, W. Minor, Center For Structural Genomics Of Infe Diseases (Csgid)
Date :  13 Sep 12  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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 And L-Ornithine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, J. Winsor, S. Grimshaw, T. Osinski, M. D. Chordia, W. F. Anderson, W. Minor
Structural Studies Of Ornithine Carbamoyltransferase From Various Pathogens
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
    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  (5, 33)

Asymmetric/Biological Unit (5, 33)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2CP3Ligand/IonPHOSPHORIC ACID MONO(FORMAMIDE)ESTER
3NVA3Ligand/IonNORVALINE
4PE53Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
5PEG18Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:168 , ASN A:169 , ASP A:233 , SER A:237 , MET A:238 , LEU A:276 , CP A:402 , HOH A:514 , HOH B:503BINDING SITE FOR RESIDUE NVA A 401
02AC2SOFTWARESER 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 , NVA A:401 , GLN B:84BINDING SITE FOR RESIDUE CP A 402
03AC3SOFTWAREGLU A:307 , HOH A:676 , ALA B:120 , PHE B:121 , ARG B:186 , THR B:215 , GLU B:222BINDING SITE FOR RESIDUE PE5 A 403
04AC4SOFTWAREGLU A:218 , ASN A:219 , VAL A:220 , HOH A:573 , HOH A:590BINDING SITE FOR RESIDUE PEG A 404
05AC5SOFTWAREASP A:132 , MET A:238 , GLY A:239 , GLU A:240BINDING SITE FOR RESIDUE PEG A 405
06AC6SOFTWARELYS A:263 , ASN A:267 , PRO A:268 , HIS A:310BINDING SITE FOR RESIDUE PEG A 406
07AC7SOFTWARELEU A:13 , PHE A:134 , SER A:173 , HOH A:505BINDING SITE FOR RESIDUE CL A 407
08AC8SOFTWARETHR A:215 , GLU A:222BINDING SITE FOR RESIDUE PEG A 408
09AC9SOFTWAREGLU A:116 , ASN A:260 , GLN A:264 , HOH A:575BINDING SITE FOR RESIDUE PEG A 409
10BC1SOFTWARELYS A:253 , GLN A:256 , ASN A:258 , HOH A:542BINDING SITE FOR RESIDUE PEG A 410
11BC2SOFTWAREASN A:258 , MET A:259 , THR A:302BINDING SITE FOR RESIDUE CL A 411
12BC3SOFTWAREARG A:96 , GLN A:225 , HOH A:617 , PHE C:306 , GLU C:307 , SER C:311 , PHE C:314 , HOH C:612BINDING SITE FOR RESIDUE PEG A 412
13BC4SOFTWAREASP A:30BINDING SITE FOR RESIDUE PEG A 413
14BC5SOFTWAREASN B:168 , ASN B:169 , ASP B:233 , SER B:237 , MET B:238 , LEU B:276 , CP B:402 , HOH B:515 , HOH C:531BINDING SITE FOR RESIDUE NVA B 401
15BC6SOFTWARESER B:57 , THR B:58 , ARG B:59 , THR B:60 , ARG B:108 , HIS B:135 , GLN B:138 , CYS B:275 , LEU B:276 , ARG B:320 , NVA B:401 , GLN C:84BINDING SITE FOR RESIDUE CP B 402
16BC7SOFTWAREALA B:205 , GLN B:209 , LYS B:253 , PHE B:294 , HOH B:637BINDING SITE FOR RESIDUE PEG B 403
17BC8SOFTWARELEU B:13 , PHE B:134 , SER B:173BINDING SITE FOR RESIDUE CL B 404
18BC9SOFTWARELEU B:262 , ASN B:267 , HIS B:310BINDING SITE FOR RESIDUE PEG B 405
19CC1SOFTWAREASN B:258 , MET B:259 , THR B:302 , GLU B:304BINDING SITE FOR RESIDUE CL B 406
20CC2SOFTWAREGLU A:283 , THR A:285 , GLY B:86BINDING SITE FOR RESIDUE PEG B 407
21CC3SOFTWAREALA B:156 , ASP B:157 , ILE B:158 , GLY B:182 , GLY B:211BINDING SITE FOR RESIDUE PEG B 408
22CC4SOFTWAREALA B:29 , LYS B:32 , GLU B:148BINDING SITE FOR RESIDUE PEG B 409
23CC5SOFTWAREASP B:132 , ARG B:167 , MET B:238 , GLY B:239BINDING SITE FOR RESIDUE PE5 B 410
24CC6SOFTWARESER B:17 , THR B:18 , LYS B:180 , LYS B:253BINDING SITE FOR RESIDUE PEG B 411
25CC7SOFTWAREHOH A:540 , ASN C:168 , ASN C:169 , ASP C:233 , SER C:237 , MET C:238 , LEU C:276 , CP C:403 , HOH C:511BINDING SITE FOR RESIDUE NVA C 401
26CC8SOFTWARELEU C:13 , SER C:173BINDING SITE FOR RESIDUE CL C 402
27CC9SOFTWAREGLN A:84 , SER 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 , NVA C:401BINDING SITE FOR RESIDUE CP C 403
28DC1SOFTWAREASP C:132 , ARG C:167 , MET C:238 , HOH C:526BINDING SITE FOR RESIDUE PE5 C 404
29DC2SOFTWARETHR C:215 , GLU C:222BINDING SITE FOR RESIDUE PEG C 405
30DC3SOFTWARELEU C:262 , ASN C:267 , HIS C:310BINDING SITE FOR RESIDUE PEG C 406
31DC4SOFTWAREGLN A:264BINDING SITE FOR RESIDUE PEG C 407
32DC5SOFTWAREASN C:258 , MET C:259 , THR C:302 , GLU C:304BINDING SITE FOR RESIDUE CL C 408
33DC6SOFTWARESER C:237 , MET C:238 , GLY C:239 , GLU C:240 , HOH C:514 , HOH C:546 , HOH C:591BINDING SITE FOR RESIDUE PEG C 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H31)

(-) 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 4H31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H31)

(-) Exons   (0, 0)

(no "Exon" information available for 4H31)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4h31a1 A:-1-152 automated matches                                                                                                                        d4h31a2 A:153-333 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
                 4h31 A  -1 NAMAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLG 333
                                     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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4h31b1 B:1-152 automated matches                                                                                                                       d4h31b2 B:153-333 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....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h31 B   1 MAFNLRNRNFLKLLDFSTKEIQFLIDLSADLKKAKYAGTEQKKLLGKNIALIFEKASTRTRCAFEVAAFDQGAQVTYIGPSGSQIGDKESMKDTARVLGRMYDGIQYRGFGQAIVEELGAFAGVPVWNGLTDEFHPTQILADFLTMLEHSQGKALADIQFAYLGDARNNVGNSLMVGAAKMGMDIRLVGPQAYWPDEELVAACQAIAKQTGGKITLTENVAEGVQGCDFLYTDVWVSMGESPEAWDERVALMKPYQVNMNVLKQTGNPNVKFMHCLPAFHNDETTIGKQVADKFGMKGLEVTEEVFESEHSIVFDEAENRMHTIKAVMVATLG 333
                                    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   


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4h31c1 C:1-152 automated matches                                                                                                                       d4h31c2 C:153-334 automated matches                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee.........hhhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhhh......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h31 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 4H31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H31)

(-) 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)

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        OTC_VIBVU | Q8DCF5: 3upd 4jfr 4jhx 4jqo 4kwt

(-) Related Entries Specified in the PDB File

3upd 2.9 ANGSTROM CRYSTAL STRUCTURE OF ORNITHINE CARBAMOYLTRANSFERASE (ARGF) FROM VIBRIO VULNIFICUS RELATED ID: CSGID-IDP91384 RELATED DB: TARGETTRACK