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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AGMATINE UREOHYDROLASE OF THERMOPLASMA VOLCANIUM
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  14 Dec 10  (Deposition) - 19 Jan 11  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Agmatine Ureohydrolase Of Thermoplasma Volcanium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AGMATINE UREOHYDROLASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL(P)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TV0538, TVG0528110
    Organism Scientific: THERMOPLASMA VOLCANIUM GSS1
    Organism Taxid: 273116
    Strain: ATCC 51530

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
1MN6Ligand/IonMANGANESE (II) ION
2MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 42)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE42Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:124 , ASP A:144 , ASP A:148 , ASP A:229 , MN A:315BINDING SITE FOR RESIDUE MN A 314
2AC2SOFTWAREASP A:144 , HIS A:146 , ASP A:229 , ASP A:231 , MN A:314BINDING SITE FOR RESIDUE MN A 315
3AC3SOFTWAREHIS B:124 , ASP B:144 , ASP B:148 , ASP B:229 , MN B:315BINDING SITE FOR RESIDUE MN B 314
4AC4SOFTWAREASP B:144 , HIS B:146 , ASP B:148 , ASP B:229 , ASP B:231 , MN B:314BINDING SITE FOR RESIDUE MN B 315
5AC5SOFTWAREASP C:144 , HIS C:146 , ASP C:229 , ASP C:231 , MN C:315BINDING SITE FOR RESIDUE MN C 314
6AC6SOFTWAREHIS C:124 , ASP C:144 , ASP C:148 , ASP C:229 , MN C:314BINDING SITE FOR RESIDUE MN C 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PZL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PZL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PZL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PZL)

(-) Exons   (0, 0)

(no "Exon" information available for 3PZL)

(-) 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:290
 aligned with Q97BB8_THEVO | Q97BB8 from UniProtKB/TrEMBL  Length:303

    Alignment length:290
                                    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
         Q97BB8_THEVO    11 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGMADLGDMEESEDVEYVIDTVESVVSAVMSDGKIPIMLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYMGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDMDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSMLAAKLLQVFIASREKYYK 300
               SCOP domains d3pzla_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh............hhhhh.eeeeee..........hhhhhhhhhhhhhh....ee....ee.hhh.eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.....eeeeee..................hhhhhhhhhhh...eeeeee...hhhhhhhhhhhhheeeehhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzl A  13 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGmADLGDmEESEDVEYVIDTVESVVSAVmSDGKIPImLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYmGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDmDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSmLAAKLLQVFIASREKYYK 302
                                    22        32        42        52        62        72        82 |     |92       102       112      |122       132       142       152 |     162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302
                                                                                                  84-MSE |                  111-MSE 119-MSE                            154-MSE                                                                     230-MSE                                               284-MSE              
                                                                                                        90-MSE                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with Q97BB8_THEVO | Q97BB8 from UniProtKB/TrEMBL  Length:303

    Alignment length:293
                                    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   
         Q97BB8_THEVO    11 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGMADLGDMEESEDVEYVIDTVESVVSAVMSDGKIPIMLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYMGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDMDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSMLAAKLLQVFIASREKYYKEHI 303
               SCOP domains d3pzlb_ B: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeee..........hhhhhhhhhhhhhh...........hhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhh....eeeeee..................hhhhhhhhhhh...eeeee....hhhhhhhhhhhhheeeehhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzl B  13 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGmADLGDmEESEDVEYVIDTVESVVSAVmSDGKIPImLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYmGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDmDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSmLAAKLLQVFIASREKYYKEHI 305
                                    22        32        42        52        62        72        82 |     |92       102       112      |122       132       142       152 |     162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302   
                                                                                                  84-MSE |                  111-MSE 119-MSE                            154-MSE                                                                     230-MSE                                               284-MSE                 
                                                                                                        90-MSE                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:290
 aligned with Q97BB8_THEVO | Q97BB8 from UniProtKB/TrEMBL  Length:303

    Alignment length:290
                                    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
         Q97BB8_THEVO    11 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGMADLGDMEESEDVEYVIDTVESVVSAVMSDGKIPIMLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYMGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDMDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSMLAAKLLQVFIASREKYYK 300
               SCOP domains d3pzlc_ C: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------Arginase-3pzlC01 C:35-296                                                                                                                                                                                                                                             ------ Pfam domains (1)
           Pfam domains (2) ----------------------Arginase-3pzlC02 C:35-296                                                                                                                                                                                                                                             ------ Pfam domains (2)
           Pfam domains (3) ----------------------Arginase-3pzlC03 C:35-296                                                                                                                                                                                                                                             ------ Pfam domains (3)
         Sec.struct. author hhhhhh..................eeeeee..........hhhhhhhhhhhhhh....eehhhhee.hhh.eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhheeeehhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh................hhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzl C  13 ASELRSIFSLKKIADAVNGYEEAKYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLESYEYSYGIDLLASGmADLGDmEESEDVEYVIDTVESVVSAVmSDGKIPImLGGEHSITVGAVRALPKDVDLVIVDAHSDFRSSYmGNKYNHACVTRRALDLLGEGRITSIGIRSVSREEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSRRVYISVDmDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSYKAVGFDIVEFSPLYDNGNTSmLAAKLLQVFIASREKYYK 302
                                    22        32        42        52        62        72        82 |     |92       102       112      |122       132       142       152 |     162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302
                                                                                                  84-MSE |                  111-MSE 119-MSE                            154-MSE                                                                     230-MSE                                               284-MSE              
                                                                                                        90-MSE
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PZL)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Arginase (56)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q97BB8_THEVO | Q97BB8)
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:0016813    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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