1ZPS - JenaLib

Title :   CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM PHOSPHORIBOSYL-AMP CYCLOHYDROLASE HISI

Authors :   J. Sivaraman, R. S. Myers, L. Boju, T. Sulea, M. Cygler, V. J. Davisson, J. D. Schrag, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Date :   17 May 05 (Deposition) - 30 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Histidine Biosynthesis, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Sivaraman, R. S. Myers, L. Boju, T. Sulea, M. Cygler, V. J. Davisson, J. D. Schrag
Crystal Structure Of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi.
Biochemistry V. 44 10071 2005
PubMed-ID: 16042384 | Reference-DOI: 10.1021/BI050472W
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 24)

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:103 , HOH A:549 , GLU B:52 , CYS B:86 , HOH B:501	BINDING SITE FOR RESIDUE CD B 2601
02	AC2	SOFTWARE	HIS B:57 , HOH B:544 , ACY B:801 , ACY B:802	BINDING SITE FOR RESIDUE CD B 2602
03	AC3	SOFTWARE	CYS A:109 , HOH A:545 , ACY A:803 , ACY A:804 , CD A:2616 , ASP B:85 , HOH B:505	BINDING SITE FOR RESIDUE CD B 2603
04	AC4	SOFTWARE	HIS B:16 , ASP B:89 , HOH B:528 , HOH B:630 , ACY B:805	BINDING SITE FOR RESIDUE CD B 2604
05	AC5	SOFTWARE	HOH A:545 , ASP B:85 , ASP B:87 , ASP B:89 , HOH B:528	BINDING SITE FOR RESIDUE CD B 2605
06	AC6	SOFTWARE	ASP A:85 , ASP A:87 , ASP A:89 , HOH A:607 , HOH B:619	BINDING SITE FOR RESIDUE CD A 2606
07	AC7	SOFTWARE	ASP A:85 , HOH A:607 , HOH A:615 , CYS B:109 , HOH B:511 , CD B:2617	BINDING SITE FOR RESIDUE CD A 2607
08	AC8	SOFTWARE	CYS A:86 , HIS B:103 , GLU B:123 , HOH B:620	BINDING SITE FOR RESIDUE CD B 2608
09	AC9	SOFTWARE	HIS B:75 , HOH B:621 , HOH B:622 , HOH B:623 , HOH B:624	BINDING SITE FOR RESIDUE CD B 2609
10	BC1	SOFTWARE	HIS A:57 , HOH A:632 , HOH A:633	BINDING SITE FOR RESIDUE CD A 2610
11	BC2	SOFTWARE	ASP A:89 , HOH A:618 , HOH B:616	BINDING SITE FOR RESIDUE CD A 2611
12	BC3	SOFTWARE	GLU B:35 , HOH B:608 , HOH B:609	BINDING SITE FOR RESIDUE CD B 2612
13	BC4	SOFTWARE	GLU A:35 , HOH A:610 , HOH A:611 , HOH A:625	BINDING SITE FOR RESIDUE CD A 2613
14	BC5	SOFTWARE	HIS A:75 , HOH A:627 , HOH A:628	BINDING SITE FOR RESIDUE CD A 2614
15	BC6	SOFTWARE	GLU B:21 , HOH B:612 , HOH B:613	BINDING SITE FOR RESIDUE CD B 2615
16	BC7	SOFTWARE	CYS A:102 , CYS A:109 , ACY A:803 , CYS B:86 , CD B:2603	BINDING SITE FOR RESIDUE CD A 2616
17	BC8	SOFTWARE	CYS A:86 , CD A:2607 , CYS B:102 , CYS B:109 , HOH B:629	BINDING SITE FOR RESIDUE CD B 2617
18	BC9	SOFTWARE	GLU A:52 , GLU A:98 , HOH A:631 , HOH A:634	BINDING SITE FOR RESIDUE CD A 2618
19	CC1	SOFTWARE	ASP A:22 , GLU A:32 , HOH A:591	BINDING SITE FOR RESIDUE CD A 2619
20	CC2	SOFTWARE	ARG A:112 , LEU B:11 , HIS B:57 , LEU B:68 , CYS B:86 , HOH B:504 , HOH B:544 , ACY B:802 , CD B:2602	BINDING SITE FOR RESIDUE ACY B 801
21	CC3	SOFTWARE	ARG A:112 , ARG B:49 , HIS B:57 , LEU B:68 , HOH B:507 , ACY B:801 , CD B:2602	BINDING SITE FOR RESIDUE ACY B 802
22	CC4	SOFTWARE	ALA A:101 , CYS A:102 , HIS A:103 , HOH A:514 , HOH A:549 , HOH A:556 , ACY A:804 , CD A:2616 , CYS B:86 , CD B:2603	BINDING SITE FOR RESIDUE ACY A 803
23	CC5	SOFTWARE	MET A:38 , VAL A:39 , TRP A:67 , CYS A:109 , HOH A:514 , HOH A:545 , ACY A:803 , CD B:2603	BINDING SITE FOR RESIDUE ACY A 804
24	CC6	SOFTWARE	ARG B:15 , HIS B:16 , ASP B:87 , ASP B:89 , CD B:2604	BINDING SITE FOR RESIDUE ACY B 805

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:124
 aligned with HIS3_METTH | O26347 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:124
                                    17        27        37        47        57        67        77        87        97       107       117       127    
           HIS3_METTH     8 VNILLNFRHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSIDGDELKVREDAVKVFDP 131
               SCOP domains d1zpsa1 A:8-131 Phosphoribosyl-AMP cyclohydrolase HisI                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........eeeeeee.....eeeeeeehhhhhhhhhhhh..eeee....eeee........eeeeeeee.....eeeeeeee..............eeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zps A   8 VNILLNFRHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSIDGDELKVREDAVKVFDP 131
                                    17        27        37        47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with HIS3_METTH | O26347 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:128
                                    13        23        33        43        53        63        73        83        93       103       113       123        
           HIS3_METTH     4 SKGDVNILLNFRHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSIDGDELKVREDAVKVFDP 131
               SCOP domains d1zpsb_ B: Phosphoribosyl-AMP cyclohydrolase HisI                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------PRA-CH-1zpsB01 B:38-112                                                    ------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------PRA-CH-1zpsB02 B:38-112                                                    ------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh...eee..eeeeeeeeee.....eeeeeeehhhhhhhhhhhh..eeee....eeee........eeeeeeee.....eeeeeeee..............eeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zps B   4 SKGDVNILLNFRHNINGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDVLVDCDGDAVVLKVEQEGGACHTGYRSCFYRSIDGDELKVREDAVKVFDP 131
                                    13        23        33        43        53        63        73        83        93       103       113       123

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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)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HIS3_METTH | O26347)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004635	phosphoribosyl-AMP cyclohydrolase activity	Catalysis of the reaction: 1-(5-phosphonatoribosyl)-5'-AMP + H(2)O = 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0000105	histidine biosynthetic process	The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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