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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUCCINYLGLUTAMATE DESUCCINYLASE FROM CHROMOBACTERIUM VIOLACEUM, NORTHEAST STRUCTURAL GENOMICS TARGET CVR22.
 
Authors :  F. Forouhar, M. Abashidze, K. Conover, T. B. Acton, G. T. Montelione, L. J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  17 Feb 05  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, K. Conover, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Succinylglutamate Desuccinylase From Chromobacterium Violaceum, Northeast Structural Genomics Target Cvr22.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUCCINYLGLUTAMATE DESUCCINYLASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ASTE
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 243365
    Strain: ATCC 12472

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , GLU A:59 , HIS A:149 , HOH A:666BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS B:56 , GLU B:59 , HIS B:149 , HOH B:603BINDING SITE FOR RESIDUE ZN B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YW4)

(-) Exons   (0, 0)

(no "Exon" information available for 1YW4)

(-) 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:319
 aligned with ASTE_CHRVO | Q7NU26 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:331
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331 
           ASTE_CHRVO     2 THSPSFLQHALSSSDTRAEWPLPGGLAARWLAPGCVELNGDARGADSVLLSCGVHGNETAPIEVVDGMLTDIAAGQLALNCRLLVMFANLDAIRQGVRYGNYDMNRLFNGAHARHPELPESVRAAELETLAAEFFAGARARKLHYDLHTAIRGSVFEKFAIYPFLHDGRTHKREQLAWLQRCGIEAVLLHTQPANTFSYFTSQYCEADAFTLELGKARPFGQNDLSRFSGIDGALRGLLSNPQANVPDLDEDKLPLFRAKYDLVKHSEAFKLNLADSVENFTLLPDGMLIAEDGAVRYQATGGEERILFPNPAVKPGLRAGIVVEPARLPS 332
               SCOP domains d1yw4a1 A:2-332 Succinylglutamate desuccinylase AstE                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh......eeee...eeeeeee..eeee........eeeeee......hhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhh......hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeeeee........eeee....--...hhhhhhhhhh....eeee......hhhhhhhhhh..eeeeeeeee.......hhhhhhhhhhhhhhhhhh..............eeeeeeeee...--............ee........--------......eee..........eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw4 A   2 THSPSFLQHALSSSDTRAEWPLPGGLAARWLAPGCVELNGDARGADSVLLSCGVHGNETAPIEVVDGmLTDIAAGQLALNCRLLVmFANLDAIRQGVRYGNYDmNRLFNGAHARHPELPESVRAAELETLAAEFFAGARARKLHYDLHTAIRGSVFEKFAIYPFLH--RTHKREQLAWLQRCGIEAVLLHTQPANTFSYFTSQYCEADAFTLELGKARPFGQNDLSRFSGIDGALRGLLSNPQANVPDLDEDKLPLFRAKYDLVKHS--FKLNLADSVENFTLLPDGmLIA--------ATGGEERILFPNPAVKPGLRAGIVVEPARLPS 332
                                    11        21        31        41        51        61       |71        81     |  91       101   |   111       121       131       141       151       161     | 171       181       191       201       211       221       231       241       251       261      |271       281       291|      301       311       321       331 
                                                                                              69-MSE            87-MSE           105-MSE                                                       167  |                                                                                               268  |               289-MSE     301                               
                                                                                                                                                                                                  170                                                                                                  271                  292                                        


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with ASTE_CHRVO | Q7NU26 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           ASTE_CHRVO     4 SPSFLQHALSSSDTRAEWPLPGGLAARWLAPGCVELNGDARGADSVLLSCGVHGNETAPIEVVDGMLTDIAAGQLALNCRLLVMFANLDAIRQGVRYGNYDMNRLFNGAHARHPELPESVRAAELETLAAEFFAGARARKLHYDLHTAIRGSVFEKFAIYPFLHDGRTHKREQLAWLQRCGIEAVLLHTQPANTFSYFTSQYCEADAFTLELGKARPFGQNDLSRFSGIDGALRGLLSNPQANVPDLDEDKLPLFRAKYDLVKHSEAFKLNLADSVENFTLLPDGMLIAEDGAVRYQATGGEERILFPNPAVKPGLRAGIVVEPARLP 331
               SCOP domains d1yw4b_ B: Succinylglutamate desuccinylase AstE                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------AstE_AspA-1yw4B01 B:46-329                                                                                                                                                                                                                                                                  -- Pfam domains (1)
           Pfam domains (2) ------------------------------------------AstE_AspA-1yw4B02 B:46-329                                                                                                                                                                                                                                                                  -- Pfam domains (2)
         Sec.struct. author ..hhhhhhh.......eee.hhh.eeeeee..eeee........eeeeee......hhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhh......hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeeeee........eeeee.hhhhh..hhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeeeeee.......hhhhhhhhhhhhhhhhhh........hhhhh.eeeeee...-------..........ee........-----.........eee....-------..eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw4 B   4 SPSFLQHALSSSDTRAEWPLPGGLAARWLAPGCVELNGDARGADSVLLSCGVHGNETAPIEVVDGmLTDIAAGQLALNCRLLVmFANLDAIRQGVRYGNYDmNRLFNGAHARHPELPESVRAAELETLAAEFFAGARARKLHYDLHTAIRGSVFEKFAIYPFLHDGRTHKREQLAWLQRCGIEAVLLHTQPANTFSYFTSQYCEADAFTLELGKARPFGQNDLSRFSGIDGALRGLLSNPQANVPDLDEDKLPLFRAKYDLV-------LNLADSVENFTLLPDGmLIA-----RYQATGGEERILFPNP-------AGIVVEPARLP 331
                                    13        23        33        43        53        63     |  73        83   |    93       103 |     113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 |     273       283     |  |-    |  303       313       323        
                                                                                            69-MSE            87-MSE           105-MSE                                                                                                                                                         265     273             289-MSE  298            313     321          
                                                                                                                                                                                                                                                                                                                          292
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YW4)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ASTE_CHRVO | Q7NU26)
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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0009017    succinylglutamate desuccinylase activity    Catalysis of the reaction: N-succinyl-L-glutamate + H(2)O = L-glutamate + succinate.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019544    arginine catabolic process to glutamate    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including glutamate.
    GO:0019545    arginine catabolic process to succinate    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including succinate.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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