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(-) Description

Title :  PZ PEPTIDASE A
 
Authors :  H. Nakano
Date :  25 Apr 10  (Deposition) - 25 Aug 10  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kawasaki, H. Nakano, A. Hosokawa, T. Nakatsu, H. Kato, K. Watanabe
The Exquisite Structure And Reaction Mechanism Of Bacterial Pz-Peptidase A Toward Collagenous Peptides: X-Ray Crystallographic Structure Analysis Of Pz-Peptidase A Reveals Differences From Mammalian Thimet Oligopeptidase.
J. Biol. Chem. V. 285 34972 2010
PubMed-ID: 20817732  |  Reference-DOI: 10.1074/JBC.M110.141838

(-) Compounds

Molecule 1 - OLIGOPEPTIDASE
    Chains: A, B
    Fragment: PEPTIDASE
    Organism Scientific: GEOBACILLUS SP. MO-1
    Organism Taxid: 295930
    Synonym: PZ PEPTIDASE A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:356 , HIS A:360 , GLU A:384 , SER A:387 , HOH A:790 , HOH A:797BINDING SITE FOR RESIDUE ZN A 565
2AC2SOFTWAREARG A:47 , VAL A:88 , HOH A:701 , HOH A:902 , HOH A:987BINDING SITE FOR RESIDUE ACT A 566
3AC3SOFTWAREGLN A:477 , HIS A:479 , TYR A:487 , TYR A:490BINDING SITE FOR RESIDUE ACT A 567
4AC4SOFTWAREHIS B:356 , HIS B:360 , GLU B:384 , SER B:387 , HOH B:789 , HOH B:801BINDING SITE FOR RESIDUE ZN B 565
5AC5SOFTWAREARG B:171 , LYS B:265 , TYR B:267 , HOH B:773 , HOH B:1139BINDING SITE FOR RESIDUE ACT B 566
6AC6SOFTWAREARG B:47 , VAL B:88 , HOH B:575 , HOH B:735BINDING SITE FOR RESIDUE ACT B 567

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AHM)

(-) 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:564
 aligned with Q4W803_9BACI | Q4W803 from UniProtKB/TrEMBL  Length:564

    Alignment length:564
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560    
         Q4W803_9BACI     1 MKFSEFRYERPNIEKLKASFQQALQSFQKASNAEEQNEAMKEINQLRNDFSTMAQICYIRHTIDTNDEFYKQEQDFFDEVEPIVKGLVNDYYRALVSSPFRSQLEGKWGKQLFALAEAELKTYSPDIVEDLQLENKLTSEYTKLVASAKIFFEGEERTLAQLQPFVESPDRDMRKRASEARFTFFQEHEEKFDEIYDQLVKVRTAIAQKLGFKNFVELGYARLGRTDYNAEMVAKFRKQVEKHIVPIAVKLRERQRERIGVEKLKYYDEAFVFPTGNPMPKGDANWIIENGKKMYEELSPETGEFFRYMIEHELMDLVAKKGKASGGYCTYIENYKAPFIFSNFTGTSGDIDVLTHEAGHAFQVYESRHYEIPEYNWPTLEACEIHSMSMEFFTWPWMKLFFKEDAEKYQFYHLSDALLFLPYGVAVDEFQHFVYENPNATPAERKQAWRAIERKYMPTKDYDGNDYLERGGFWQRQSHIYTTAFYYIDYTLAQICAFQFWKRSRENYKEAWNDYLTLCRQGGSKPFTELVRVANLISPFEDGCVQSVVGGIEGWLNSVDDQSL 564
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.........eeeeehhhheeeeeeee...hhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ahm A   1 MKFSEFRYERPNIEKLKASFQQALQSFQKASNAEEQNEAMKEINQLRNDFSTMAQICYIRHTIDTNDEFYKQEQDFFDEVEPIVKGLVNDYYRALVSSPFRSQLEGKWGKQLFALAEAELKTYSPDIVEDLQLENKLTSEYTKLVASAKIFFEGEERTLAQLQPFVESPDRDMRKRASEARFTFFQEHEEKFDEIYDQLVKVRTAIAQKLGFKNFVELGYARLGRTDYNAEMVAKFRKQVEKHIVPIAVKLRERQRERIGVEKLKYYDEAFVFPTGNPMPKGDANWIIENGKKMYEELSPETGEFFRYMIEHELMDLVAKKGKASGGYCTYIENYKAPFIFSNFTGTSGDIDVLTHEAGHAFQVYESRHYEIPEYNWPTLEACEIHSMSMEFFTWPWMKLFFKEDAEKYQFYHLSDALLFLPYGVAVDEFQHFVYENPNATPAERKQAWRAIERKYMPTKDYDGNDYLERGGFWQRQSHIYTTAFYYIDYTLAQICAFQFWKRSRENYKEAWNDYLTLCRQGGSKPFTELVRVANLISPFEDGCVQSVVGGIEGWLNSVDDQSL 564
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560    


Chain B from PDB  Type:PROTEIN  Length:563
 aligned with Q4W803_9BACI | Q4W803 from UniProtKB/TrEMBL  Length:564

    Alignment length:563
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561   
         Q4W803_9BACI     2 KFSEFRYERPNIEKLKASFQQALQSFQKASNAEEQNEAMKEINQLRNDFSTMAQICYIRHTIDTNDEFYKQEQDFFDEVEPIVKGLVNDYYRALVSSPFRSQLEGKWGKQLFALAEAELKTYSPDIVEDLQLENKLTSEYTKLVASAKIFFEGEERTLAQLQPFVESPDRDMRKRASEARFTFFQEHEEKFDEIYDQLVKVRTAIAQKLGFKNFVELGYARLGRTDYNAEMVAKFRKQVEKHIVPIAVKLRERQRERIGVEKLKYYDEAFVFPTGNPMPKGDANWIIENGKKMYEELSPETGEFFRYMIEHELMDLVAKKGKASGGYCTYIENYKAPFIFSNFTGTSGDIDVLTHEAGHAFQVYESRHYEIPEYNWPTLEACEIHSMSMEFFTWPWMKLFFKEDAEKYQFYHLSDALLFLPYGVAVDEFQHFVYENPNATPAERKQAWRAIERKYMPTKDYDGNDYLERGGFWQRQSHIYTTAFYYIDYTLAQICAFQFWKRSRENYKEAWNDYLTLCRQGGSKPFTELVRVANLISPFEDGCVQSVVGGIEGWLNSVDDQSL 564
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.........eeeeehhhheeeeeeee...hhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ahm B   2 KFSEFRYERPNIEKLKASFQQALQSFQKASNAEEQNEAMKEINQLRNDFSTMAQICYIRHTIDTNDEFYKQEQDFFDEVEPIVKGLVNDYYRALVSSPFRSQLEGKWGKQLFALAEAELKTYSPDIVEDLQLENKLTSEYTKLVASAKIFFEGEERTLAQLQPFVESPDRDMRKRASEARFTFFQEHEEKFDEIYDQLVKVRTAIAQKLGFKNFVELGYARLGRTDYNAEMVAKFRKQVEKHIVPIAVKLRERQRERIGVEKLKYYDEAFVFPTGNPMPKGDANWIIENGKKMYEELSPETGEFFRYMIEHELMDLVAKKGKASGGYCTYIENYKAPFIFSNFTGTSGDIDVLTHEAGHAFQVYESRHYEIPEYNWPTLEACEIHSMSMEFFTWPWMKLFFKEDAEKYQFYHLSDALLFLPYGVAVDEFQHFVYENPNATPAERKQAWRAIERKYMPTKDYDGNDYLERGGFWQRQSHIYTTAFYYIDYTLAQICAFQFWKRSRENYKEAWNDYLTLCRQGGSKPFTELVRVANLISPFEDGCVQSVVGGIEGWLNSVDDQSL 564
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561
   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  (0, 0)

(no "SCOP Domain" information available for 3AHM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AHM)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4W803_9BACI | Q4W803)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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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  3ahm
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q4W803_9BACI | Q4W803: 3ahn 3aho

(-) Related Entries Specified in the PDB File

3ahn 3aho