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(-) Description

Title :  THE STRUCTURE OF PREDICTED METAL-DEPENDENT HYDROLASE FROM BACILLUS STEAROTHERMOPHILUS
 
Authors :  J. Maderova, D. Borek, D. Tomchick, A. Joachimiak, F. Collart, Z. Otwinowski, Midwest Center For Structural Genomics (Mcsg)
Date :  14 Oct 03  (Deposition) - 30 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Zinc-Dependent Hydrolase, Structural Genomics, Cyclase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Maderova, D. Borek, D. Tomchick, A. Joachimiak, F. Collart, Z. Otwinowski
The Structure Of Potential Metal-Dependent Hydrolase With Cyclase Activity
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METAL-DEPENDENT HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1SO424Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:51 , HIS A:155 , GLU A:167BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREHIS B:45 , HIS B:49 , ASP B:51 , HIS B:55 , HIS B:155 , GLU B:167 , HOH B:2099BINDING SITE FOR RESIDUE ZN B 1002
03AC3SOFTWAREMET A:1 , ARG A:203 , ARG B:203BINDING SITE FOR RESIDUE SO4 A 2001
04AC4SOFTWARETYR A:17 , LYS A:18 , LYS A:20 , HOH A:2132BINDING SITE FOR RESIDUE SO4 A 2002
05AC5SOFTWARELYS B:18 , ARG B:147 , ALA B:148 , HOH B:2100 , HOH B:2104BINDING SITE FOR RESIDUE SO4 B 2003
06AC6SOFTWARELYS A:20 , GLU A:22 , ARG A:128BINDING SITE FOR RESIDUE SO4 A 2004
07AC7SOFTWAREHIS B:82 , ASN B:84 , HOH B:2071BINDING SITE FOR RESIDUE SO4 B 2005
08AC8SOFTWAREGLU A:112 , ASP A:113 , ALA A:114 , HIS A:116 , HOH A:2094BINDING SITE FOR RESIDUE SO4 A 2006
09AC9SOFTWAREGLU B:112 , ASP B:113 , ALA B:114 , HIS B:116BINDING SITE FOR RESIDUE SO4 B 2007
10BC1SOFTWAREASP B:113 , ARG B:170 , HOH B:2060 , HOH B:2073BINDING SITE FOR RESIDUE SO4 B 2008
11BC2SOFTWARELYS A:18 , ARG A:147 , ALA A:148BINDING SITE FOR RESIDUE SO4 A 2009
12BC3SOFTWAREHIS B:116 , PHE B:117 , GLU B:118BINDING SITE FOR RESIDUE SO4 B 2010
13BC4SOFTWAREARG B:178BINDING SITE FOR RESIDUE SO4 B 2011
14BC5SOFTWAREASN B:109 , GLU B:112 , ASP B:113 , ALA B:114 , PHE B:115 , LEU B:143 , ARG B:170 , HOH B:2023 , HOH B:2088 , HOH B:2107BINDING SITE FOR RESIDUE SO4 B 2012

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R61)

(-) Exons   (0, 0)

(no "Exon" information available for 1R61)

(-) 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:205
 aligned with P84132_GEOSE | P84132 from UniProtKB/TrEMBL  Length:207

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
         P84132_GEOSE     1 AAMKVYDVTAPIYEGMPVYKNKPEKQPKRTTITNGYVTESRIDMDVHTGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLFKTKNSFEDAFHFEFIFVAEDAARYLADKQIRGVGIDALGIERAQEGHPTHKTLFSAGVIIIEGLRLKDVPEGRYFMVAAPLKLVGTDAAPARVLLFDR 205
               SCOP domains d1r61a_ A: Unnamed protein                                                                                                                                                                                    SCOP domains
               CATH domains 1r61A00 A:-1-203 Putative cyclase                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........hhhhhhhhh.eeeeeee..eeeeeeeee.....eee.hhhhh..............eeeeeeee......eehhhhhh........eeeeehhhhhh........eehhhhhhhhhhhh..eee............hhhhhhhhhh..eeee.........eeeeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r61 A  -1 AAMKVYDVTAPIYEGMPVYKNKPEKQPKRTTITNGYVTESRIDMDVHTGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLFKTKNSFEDAFHFEFIFVAEDAARYLADKQIRGVGIDALGIERAQEGHPTHKTLFSAGVIIIEGLRLKDVPEGRYFMVAAPLKLVGTDAAPARVLLFDR 203
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with P84132_GEOSE | P84132 from UniProtKB/TrEMBL  Length:207

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
         P84132_GEOSE     1 AAMKVYDVTAPIYEGMPVYKNKPEKQPKRTTITNGYVTESRIDMDVHTGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLFKTKNSFEDAFHFEFIFVAEDAARYLADKQIRGVGIDALGIERAQEGHPTHKTLFSAGVIIIEGLRLKDVPEGRYFMVAAPLKLVGTDAAPARVLLFDR 205
               SCOP domains d1r61b_ B: Unnamed protein                                                                                                                                                                                    SCOP domains
               CATH domains 1r61B00 B:-1-203 Putative cyclase                                                                                                                                                                             CATH domains
           Pfam domains (1) ----Cyclase-1r61B01 B:3-149                                                                                                                            ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----Cyclase-1r61B02 B:3-149                                                                                                                            ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....eee..........hhhhhhhhh.eee..........eeeee.....eee.hhhh.....hhhhhhhhh.eeeeeeee......eehhhhhh........eeeeehhhhhh........eehhhhhhhhhhhh..eeee...........hhhhhhhhhh..eeee.........eeeeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r61 B  -1 AAMKVYDVTAPIYEGMPVYKNKPEKQPKRTTITNGYVTESRIDMDVHTGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLFKTKNSFEDAFHFEFIFVAEDAARYLADKQIRGVGIDALGIERAQEGHPTHKTLFSAGVIIIEGLRLKDVPEGRYFMVAAPLKLVGTDAAPARVLLFDR 203
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Cyclase] (2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P84132_GEOSE | P84132)
molecular function
    GO:0004061    arylformamidase activity    Catalysis of the reaction: N-formyl-L-kynurenine + H2O = formate + L-kynurenine.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019441    tryptophan catabolic process to kynurenine    The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine.

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  1r61
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        P84132_GEOSE | P84132: 3krv

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