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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOHYDROLASE FROM CAULOBACTER CRESCENTUS
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Alm York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  14 Sep 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Aminohydrolase, Structural Genomics, Nysgxrc, Target 9257A, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Aminohydrolase From Caulobacter Crescentus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDASE
    Atcc: 19089
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CC_2746
    Organism Scientific: CAULOBACTER CRESCENTUS
    Organism Taxid: 190650
    Strain: CB15

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  
Biological Unit 5 (1x):   C 
Biological Unit 6 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2RAG)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:279 -A:356
2B:279 -B:356
3C:279 -C:356
4D:279 -D:356

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RAG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RAG)

(-) Sequences/Alignments

Asymmetric 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:369
 aligned with Q9A4T4_CAUCR | Q9A4T4 from UniProtKB/TrEMBL  Length:417

    Alignment length:379
                                    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       336       346       356       366       376       386       396       406         
         Q9A4T4_CAUCR    37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPERKAALEALGRAPDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ragA00 A:37-415 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh....eeeee.hhhhhh..........hhhhhh...hhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....eeeeeee........eehhhhhhhhhhh..eeee.............----------.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rag A  37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPE----------APDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
                                    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      |  -       306       316       326       336       346       356       366       376       386       396       406         
                                                                                                                                                                                                                                                                                          293        304                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:369
 aligned with Q9A4T4_CAUCR | Q9A4T4 from UniProtKB/TrEMBL  Length:417

    Alignment length:379
                                    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       336       346       356       366       376       386       396       406         
         Q9A4T4_CAUCR    37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPERKAALEALGRAPDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ragB00 B:37-415 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh....eeeee.hhhhhh..........hhhhhh...hhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....eeeeeee........eehhhhhhhhhhh..eeee.............----------.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rag B  37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPE----------APDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
                                    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      |  -       306       316       326       336       346       356       366       376       386       396       406         
                                                                                                                                                                                                                                                                                          293        304                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:369
 aligned with Q9A4T4_CAUCR | Q9A4T4 from UniProtKB/TrEMBL  Length:417

    Alignment length:379
                                    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       336       346       356       366       376       386       396       406         
         Q9A4T4_CAUCR    37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPERKAALEALGRAPDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ragC00 C:37-415 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh....eeeee.hhhhhh..........hhhhhh...hhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....eeeeeee........eehhhhhhhhhhh..eeee.............----------.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rag C  37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPE----------APDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
                                    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      |  -       306       316       326       336       346       356       366       376       386       396       406         
                                                                                                                                                                                                                                                                                          293        304                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:369
 aligned with Q9A4T4_CAUCR | Q9A4T4 from UniProtKB/TrEMBL  Length:417

    Alignment length:379
                                    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       336       346       356       366       376       386       396       406         
         Q9A4T4_CAUCR    37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPERKAALEALGRAPDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ragD00 D:37-415 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) -----Peptidase_M19-2ragD01 D:42-407                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) -----Peptidase_M19-2ragD02 D:42-407                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (2)
           Pfam domains (3) -----Peptidase_M19-2ragD03 D:42-407                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (3)
           Pfam domains (4) -----Peptidase_M19-2ragD04 D:42-407                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (4)
         Sec.struct. author hhhhhhhhh....eeeee.hhhhhh..........hhhhhh...hhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh.eeee.........................hhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhh....eeeee............hhhhhhhhhhh..eeee.............----------.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rag D  37 SKADKALHDKFLTLDTHLDTPAHFGRPGWDIADHHEVEHDFSQVDLPRMNQGGLDGGFFVVYIGQGELTEKGYTYARDYALHRTIEIREMLAANPDTFEMALTSDDARRIAKAGKKFAFVSMENSWPVGEDLSLVETFYKEGLRMAGPVHFRNNQLADSSTDPKGKIWNGYSPLGLRWLAEANRLGIVIDVSHASDDVVDQSVALSKAPIIASHSGPKAVYDHPRNLDDARLKKIADAGGAICINSIYLTDTTPSPE----------APDMKTATPEAVKAYADKRAAIDKAHPAARGDFDLYMKSMLHVLKVAGPKGVCVGADWDGGGGMDGFEDITDLPKITARLKAEGYSDADIEAIWSGNVLRIVDAAQAYAKSV 415
                                    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      |  -       306       316       326       336       346       356       366       376       386       396       406         
                                                                                                                                                                                                                                                                                          293        304
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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  (0, 0)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9A4T4_CAUCR | Q9A4T4)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  2rag
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 Related Entries

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